Contacts of the helix formed by residues 109 - 130 (chain B) in PDB entry 2VN9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 109 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B TYR* 4.0 8.0 + - - -
108B TYR* 1.3 79.6 - - - +
110B GLU* 1.3 66.0 + - - +
111B ALA* 3.4 16.1 + - - +
112B ASP* 2.7 30.6 + - - +
113B ALA* 3.1 12.9 + - - +
280B SER 3.4 10.8 - - - -
281B MET* 3.5 15.1 - - - -
282B MET 3.2 20.2 - - - -
284B ARG* 4.6 5.6 - - - -
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B SER* 1.3 74.8 - - - +
111B ALA* 1.3 52.5 + - - +
113B ALA* 3.0 6.8 + - - -
114B SER* 2.7 36.0 + - - -
208B LEU* 3.9 18.8 - - + -
240B THR 3.9 1.2 - - - +
241B VAL* 3.2 15.9 - - + +
242B THR* 2.8 45.3 + - - +
245B ALA* 4.3 5.4 - - - -
271B TRP* 3.0 22.4 + - + +
279B ALA* 4.0 1.8 - - - -
280B SER* 3.2 36.3 + - - +
282B MET 4.5 1.2 + - - -
284B ARG* 4.5 14.1 + - - +
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B SER* 3.2 10.7 - - - +
110B GLU* 1.3 75.7 - - - +
112B ASP* 1.3 62.3 + - - +
115B HIS* 3.1 19.9 + - - +
275B ARG* 3.1 21.5 + - + +
276B SER* 6.2 1.3 - - - -
279B ALA* 3.5 21.1 - - + +
280B SER 3.1 12.9 + - - +
281B MET* 5.0 13.5 - - + -
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Residues in contact with ASP 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ARG* 4.3 12.4 + - - +
107B TYR* 3.8 13.6 - - - +
108B TYR* 3.3 26.5 + - + -
109B SER* 2.7 35.3 + - - +
111B ALA* 1.3 79.2 - - - +
113B ALA* 1.3 61.7 + - - +
115B HIS* 3.2 9.9 + - - +
116B CYS* 3.2 25.6 + - - -
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B TYR* 3.3 26.3 - - + +
109B SER 3.1 9.5 + - - +
110B GLU 3.0 7.3 + - - +
112B ASP* 1.3 74.1 - - - +
114B SER* 1.3 59.2 + - - +
116B CYS* 3.4 7.6 + - - +
117B ILE* 2.9 34.0 + - - +
204B LEU* 5.1 0.4 - - + -
207B LEU* 4.2 10.8 - - + -
208B LEU* 4.0 24.2 - - + -
271B TRP* 3.9 3.8 - - + -
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLU 2.7 18.4 + - - -
111B ALA* 4.3 0.4 - - - -
113B ALA* 1.3 71.6 - - - +
115B HIS* 1.3 55.2 + - - +
117B ILE* 3.6 0.9 - - - +
118B GLN* 2.7 37.9 + - - +
271B TRP* 2.7 48.5 + - - -
272B ILE* 3.6 12.6 + - - +
275B ARG* 3.4 25.1 + - - +
279B ALA* 4.4 0.4 - - - -
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Residues in contact with HIS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ALA 3.1 13.9 + - - +
112B ASP* 3.2 13.6 + - - +
114B SER* 1.3 75.9 - - - +
116B CYS* 1.3 65.1 + - - +
118B GLN* 3.6 6.3 + - - +
119B GLN* 3.0 59.4 + - + +
150B GLY* 5.8 3.4 + - - -
151B ALA 5.4 3.5 + - - -
275B ARG* 3.8 33.9 + - - +
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Residues in contact with CYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 3.6 45.8 - - + -
102B ILE* 4.7 7.6 - - - -
105B ARG* 5.0 8.7 - - - -
108B TYR* 5.5 0.2 - - - -
112B ASP 3.2 16.0 + - - -
113B ALA* 3.5 8.7 - - - +
115B HIS* 1.3 77.2 - - - +
117B ILE* 1.3 66.6 + - - +
119B GLN* 3.1 13.9 + - - +
120B ILE* 3.0 26.7 + - + +
153B VAL* 4.6 5.9 - - - +
207B LEU* 4.2 8.3 - - + -
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ALA 2.9 23.1 + - - +
114B SER* 3.9 3.1 - - - +
116B CYS* 1.3 74.0 - - - +
118B GLN* 1.3 56.4 + - - +
120B ILE* 3.7 19.3 - - + +
121B LEU* 2.8 50.3 + - + +
200B CYS* 4.3 9.0 - - + +
203B ILE* 4.1 12.3 - - + -
204B LEU* 3.8 36.8 - - + +
207B LEU* 3.7 23.3 - - + -
248B LEU* 5.0 0.2 - - + -
252B MET* 4.8 5.6 - - + -
271B TRP* 4.6 1.1 - - + -
272B ILE* 3.7 13.5 - - + -
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Residues in contact with GLN 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B SER 2.7 21.2 + - - +
115B HIS* 3.7 9.3 + - - +
117B ILE* 1.3 73.7 - - - +
119B GLN* 1.3 59.7 + - + +
121B LEU* 3.3 5.8 + - - +
122B GLU* 2.9 42.1 + - + +
267B LEU* 3.8 9.8 + - + +
272B ILE* 3.5 42.2 + - + +
273B CYS* 4.7 5.1 - - - +
275B ARG* 2.9 24.1 + - - +
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Residues in contact with GLN 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASN* 3.5 34.6 + - - +
115B HIS* 3.0 51.3 + - + +
116B CYS* 3.1 10.9 + - - +
118B GLN* 1.3 79.6 - - + +
120B ILE* 1.3 62.2 + - - +
122B GLU* 3.3 6.6 + - - +
123B SER 3.1 17.8 + - - -
151B ALA 4.2 2.7 + - - +
152B ALA* 3.2 13.0 - - - +
153B VAL* 3.0 40.1 + - + +
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Residues in contact with ILE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 4.5 12.6 - - + -
116B CYS* 3.0 19.9 + - + +
117B ILE* 3.7 27.6 - - + +
119B GLN* 1.3 74.7 - - - +
121B LEU* 1.3 62.0 + - + +
123B SER* 2.6 24.6 + - - +
124B VAL* 3.0 14.8 + - + +
137B LEU* 5.2 4.9 - - + -
142B LEU* 3.4 45.5 - - + -
153B VAL* 4.2 11.4 - - + -
200B CYS* 4.3 22.0 - - - -
203B ILE* 4.4 9.6 - - + -
207B LEU* 4.8 0.9 - - + -
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 2.8 37.2 + - + +
118B GLN 3.3 4.7 + - - +
120B ILE* 1.3 78.1 - - + +
122B GLU* 1.3 56.2 + - - +
124B VAL* 3.8 3.7 - - + +
125B ASN* 2.8 32.1 + - - +
197B MET* 3.6 36.6 - - + -
200B CYS* 4.3 11.9 - - - -
252B MET* 4.1 8.7 - - + -
263B ALA* 4.1 7.4 - - + +
266B ALA* 3.7 31.9 - - + -
267B LEU* 3.7 15.7 - - + +
272B ILE* 4.2 13.0 - - + -
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B HIS* 3.7 25.3 + - + -
72B ASN* 4.0 4.5 - - - +
118B GLN* 2.9 30.8 + - + +
119B GLN* 3.3 8.9 + - - +
121B LEU* 1.3 75.4 - - - +
123B SER* 1.3 57.6 + - - +
125B ASN* 3.9 7.0 + - - +
126B HIS* 3.1 26.9 + - - +
267B LEU* 3.6 30.5 - - + +
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B HIS* 4.2 5.8 - - - -
72B ASN* 3.2 28.2 + - - -
73B ILE* 3.8 14.6 - - - +
119B GLN 3.1 9.5 + - - -
120B ILE* 2.6 27.7 + - - +
122B GLU* 1.3 74.9 - - - +
124B VAL* 1.3 58.1 + - - +
126B HIS* 3.3 3.6 + - - +
127B CYS* 2.9 33.6 + - - -
142B LEU* 5.8 0.3 - - - +
155B LEU* 3.8 18.5 + - - +
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ILE* 3.0 17.4 + - + +
121B LEU* 3.8 6.1 - - - +
123B SER* 1.3 74.6 + - - +
125B ASN* 1.3 56.3 + - - +
127B CYS* 3.1 10.1 + - - +
128B HIS* 2.7 67.3 + - + +
134B HIS* 6.1 0.9 - - + -
137B LEU* 3.5 34.8 - - + -
155B LEU* 4.8 3.1 - - + -
196B ASP* 4.2 6.7 - - + +
197B MET* 4.1 12.1 - - - -
200B CYS* 4.3 9.2 - - - -
263B ALA* 4.0 10.3 - - + -
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Residues in contact with ASN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU 2.8 18.9 + - - +
122B GLU* 3.9 7.9 + - - +
124B VAL* 1.3 78.3 - - - +
126B HIS* 1.3 57.7 + - - +
128B HIS* 3.8 4.5 - - - +
129B LEU* 2.9 51.7 + - - +
263B ALA* 3.6 14.4 - - + +
264B SER* 2.8 34.2 + - - -
267B LEU* 4.3 16.4 - - + +
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Residues in contact with HIS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU 5.3 1.2 + - - -
68B LEU* 4.2 14.3 - - + +
69B LYS* 3.3 27.6 + - - +
70B HIS* 3.6 34.9 - + + -
73B ILE* 4.3 2.7 - - + -
122B GLU 3.1 20.1 + - - +
123B SER 3.6 4.9 - - - +
124B VAL 3.2 0.2 - - - -
125B ASN* 1.3 74.7 - - - +
127B CYS* 1.3 65.1 + - - +
129B LEU* 3.5 12.5 + - + +
130B ASN* 2.8 54.4 + - - -
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Residues in contact with CYS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 4.1 13.0 - - - -
73B ILE* 4.0 10.5 - - - -
123B SER 2.9 19.1 + - - -
124B VAL* 3.3 11.4 - - - +
126B HIS* 1.3 75.9 - - - +
128B HIS* 1.3 59.3 + - + +
130B ASN* 2.9 15.8 + - - +
132B ILE* 2.9 39.7 + - + +
134B HIS* 5.4 5.4 - - + +
155B LEU* 4.0 13.5 - - - -
158B PHE* 3.7 31.0 - - - -
196B ASP* 5.7 0.7 - - - +
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Residues in contact with HIS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B VAL* 2.7 42.5 + - + +
125B ASN* 3.9 7.4 - - - +
127B CYS* 1.3 73.9 - - + +
129B LEU* 1.3 62.4 + - - +
131B GLY 3.2 8.8 + - - -
132B ILE 3.1 21.8 - - - +
133B VAL* 4.5 0.4 - - - -
193B LYS* 3.2 79.0 + - + +
196B ASP* 2.9 27.1 + - + +
197B MET* 4.6 8.4 - - + +
263B ALA* 4.5 9.4 + - + +
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ASN* 2.9 44.1 + - - +
126B HIS* 3.7 14.8 - - + +
128B HIS* 1.3 76.3 - - - +
130B ASN* 1.3 65.4 + - - +
131B GLY 3.3 1.2 + - - -
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Residues in contact with ASN 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.7 39.1 - - + +
68B LEU* 4.1 16.6 - - + -
126B HIS* 2.8 52.8 + - - +
127B CYS 2.9 5.9 + - - +
129B LEU* 1.3 82.0 - - - +
131B GLY* 1.3 61.8 + - - +
132B ILE* 3.3 6.4 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il