Contacts of the helix formed by residues 101 - 118 (chain B) in PDB entry 3V6R
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 ASN 101 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B PHE 3.4 0.8 - - - -
100B GLN* 1.3 97.7 + - - +
102B GLN* 1.3 56.8 + - - +
103B THR* 3.1 24.6 + - - -
104B HIS* 3.1 25.6 + - - +
105B ALA* 2.8 35.4 + - - +
216B THR 5.3 1.0 - - - +
218B PHE* 3.8 27.3 - - + +
387B ILE* 3.8 11.7 - - - -
390B TRP* 5.0 0.2 - - - -
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Residues in contact with GLN 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ASN* 1.3 72.5 - - - +
103B THR* 1.3 62.2 + - + +
105B ALA* 3.4 0.7 + - - +
106B LYS* 2.8 55.5 + - - +
383B ARG 3.5 0.5 - - - +
384B GLU* 3.3 31.3 + - + +
385B HIS 2.9 37.6 + - - +
387B ILE* 4.7 3.2 - - - +
390B TRP* 3.1 33.6 + - - +
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Residues in contact with THR 103 (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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101B ASN* 3.1 11.0 + - - -
102B GLN* 1.3 81.1 - - + +
104B HIS* 1.3 63.6 + - - +
106B LYS* 3.6 11.5 + - - +
107B ARG* 3.2 29.1 + - - +
213B THR 4.9 6.1 - - - +
214B ALA* 3.5 29.6 - - - +
215B GLY* 4.5 7.2 - - - +
216B THR 4.3 13.1 + - - +
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Residues in contact with HIS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLN* 5.0 13.7 + - + -
95B LEU* 6.4 2.2 - - + -
96B SER 4.5 4.9 - - - -
98B PRO* 3.3 29.6 + - + +
100B GLN* 3.2 38.9 + - + -
101B ASN* 3.1 26.6 + - - +
103B THR* 1.3 80.6 + - - +
105B ALA* 1.4 61.4 + - - +
107B ARG* 3.7 5.1 + - - +
108B ALA* 3.3 20.1 + - - +
218B PHE 5.8 5.6 - - - -
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Residues in contact with ALA 105 (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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98B PRO 3.1 15.7 + - - +
99B PHE* 3.8 11.0 - - - -
101B ASN 2.8 20.9 + - - +
102B GLN 3.8 0.2 - - - +
104B HIS* 1.4 71.7 - - - +
106B LYS* 1.3 58.7 + - - +
108B ALA 3.5 0.3 + - - -
109B TYR* 2.9 34.1 + - - +
390B TRP* 3.5 37.7 - - + -
394B ILE* 3.8 5.6 - - + +
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Residues in contact with LYS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLN* 2.8 55.6 + - - +
103B THR* 3.8 11.1 - - - +
105B ALA* 1.3 72.1 - - - +
107B ARG* 1.4 56.7 + - + +
109B TYR* 4.1 1.6 - - - +
110B ARG* 3.0 33.2 + - - +
211B ALA* 5.9 3.4 - - + -
213B THR* 2.8 42.9 + - + +
381B ASP 5.4 4.0 - - - +
382B GLU* 3.3 32.5 + - - +
383B ARG 5.2 0.8 - - - -
384B GLU 5.5 0.2 - - - +
390B TRP* 4.0 23.0 - - + -
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLN* 5.6 10.9 - - - +
93B LYS* 4.7 9.5 - - - +
103B THR 3.2 18.0 + - - +
104B HIS* 3.8 6.5 - - - +
105B ALA 3.3 0.2 - - - -
106B LYS* 1.4 76.1 - - + +
108B ALA* 1.4 57.6 + - - +
110B ARG* 3.3 10.2 + - - +
111B GLU* 2.8 61.6 + - - +
207B ASP* 4.7 18.6 + - - +
208B PHE 5.6 0.4 - - - +
209B GLY 4.2 11.9 + - - -
210B LEU* 3.7 44.9 - - + +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 4.5 21.2 - - + +
98B PRO* 3.4 33.7 - - + -
104B HIS* 3.3 13.7 + - - +
105B ALA 4.0 2.7 - - - +
107B ARG* 1.4 77.2 - - - +
109B TYR* 1.4 57.9 + - - +
111B GLU* 4.0 5.6 - - - +
112B LEU* 3.1 32.9 + - - +
144B LEU* 6.1 0.2 - - - +
394B ILE* 4.4 6.3 - - + -
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Residues in contact with TYR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ALA 2.9 19.8 + - - +
106B LYS 4.1 1.8 - - - +
108B ALA* 1.4 77.3 - - - +
110B ARG* 1.4 61.7 + - + +
112B LEU* 3.4 4.9 + - - +
113B VAL* 3.0 48.3 + - + +
380B LEU 4.8 14.3 + - - -
381B ASP* 5.5 8.5 - - + -
390B TRP* 3.9 21.5 - + + -
393B LEU* 3.9 33.7 - - + +
394B ILE* 3.9 20.3 - - + +
397B GLU* 3.6 38.1 + - + -
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Residues in contact with ARG 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LYS* 3.0 21.4 + - - +
107B ARG* 3.8 10.0 + - - +
109B TYR* 1.4 81.9 - - + +
111B GLU* 1.4 52.7 + - - +
113B VAL* 3.4 4.9 + - - +
114B LEU* 2.8 59.5 + - + +
185B ILE* 3.9 15.2 - - - +
186B ILE 5.2 2.0 + - - -
208B PHE* 2.8 35.8 + - - +
209B GLY 2.7 26.5 + - - -
210B LEU* 4.5 12.7 + - - +
211B ALA* 4.5 17.4 - - - +
381B ASP* 4.9 27.6 + - + +
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LYS* 2.9 32.3 + - - -
95B LEU* 4.5 6.9 - - - +
107B ARG* 2.8 40.7 + - - +
108B ALA* 4.0 5.3 - - - +
110B ARG* 1.4 73.7 - - - +
112B LEU* 1.3 57.7 + - - +
115B MET* 2.9 49.3 + - - +
144B LEU* 3.6 20.9 - - + +
206B LEU 4.5 6.1 - - - +
207B ASP* 4.4 16.6 - - - +
208B PHE* 3.9 17.9 - - + -
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU* 6.1 1.1 - - + -
108B ALA 3.1 20.4 + - - +
109B TYR* 3.4 4.2 + - - +
111B GLU* 1.3 75.7 - - - +
113B VAL* 1.3 61.5 + - - +
115B MET* 4.3 3.2 - - - +
116B LYS* 3.4 23.7 + - + +
126B LEU* 4.3 10.2 - - + +
129B VAL* 3.8 18.8 - - + -
142B VAL* 4.5 7.0 - - + -
144B LEU* 3.7 28.2 - - + +
394B ILE* 4.1 16.4 - - + +
397B GLU* 3.8 32.5 - - + +
398B VAL* 3.8 22.0 - - + -
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 3.0 44.5 + - + +
110B ARG* 3.8 6.1 - - - +
112B LEU* 1.3 73.5 - - - +
114B LEU* 1.3 67.9 + - + +
116B LYS* 3.4 4.9 + - - +
117B CYS* 3.0 41.3 + - - -
397B GLU* 3.6 34.8 - - + +
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Residues in contact with LEU 114 (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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110B ARG* 2.8 51.6 + - + +
113B VAL* 1.3 77.6 - - + +
115B MET* 1.4 58.4 + - - +
117B CYS* 4.5 5.4 - - + +
118B VAL* 2.9 41.1 + - + +
185B ILE* 3.8 27.8 - - + -
208B PHE* 3.7 45.8 - - + -
373B PRO* 6.4 0.4 - - + -
374B GLN 5.7 0.2 - - - +
375B ILE 4.0 17.7 - - - +
381B ASP* 5.6 5.2 - - - +
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Residues in contact with MET 115 (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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111B GLU* 2.9 33.3 + - - +
112B LEU* 4.3 2.7 - - - +
114B LEU* 1.4 75.2 - - - +
116B LYS* 1.4 59.6 + - - +
118B VAL* 3.5 13.3 - - - +
119B ASN* 5.1 0.3 - - - +
124B ILE* 3.9 22.8 - - + +
125B SER* 3.7 31.8 - - - +
126B LEU* 3.7 45.0 + - + +
144B LEU* 4.6 8.7 - - - -
146B MET* 4.0 27.1 - - + +
206B LEU 4.9 2.2 - - - +
208B PHE* 3.5 25.9 - - + -
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Residues in contact with LYS 116 (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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112B LEU* 3.4 17.9 + - + +
113B VAL* 3.6 5.6 - - - +
114B LEU 3.2 0.8 - - - -
115B MET* 1.4 79.0 - - - +
117B CYS* 1.4 66.1 + - - +
118B VAL 3.9 3.5 - - - +
119B ASN* 3.9 11.1 + - - +
126B LEU* 4.5 17.0 - - + +
397B GLU* 5.8 2.2 - - - +
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Residues in contact with CYS 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 VAL* 3.0 31.5 + - + +
114B LEU* 4.3 6.7 - - + +
116B LYS* 1.4 74.9 - - - +
118B VAL* 1.4 64.0 + - + +
119B ASN* 3.4 12.8 + - - -
373B PRO* 3.9 7.2 - - + +
374B GLN* 3.3 53.9 + - + +
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B LEU* 2.9 36.5 + - + +
115B MET* 3.5 14.5 - - - +
117B CYS* 1.4 71.3 - - + +
119B ASN* 1.3 71.9 + - - +
120B HIS 4.1 3.4 - - - +
123B ILE* 3.7 32.3 - - + -
124B ILE 5.5 1.1 - - - +
125B SER* 5.1 5.5 - - - -
179B HIS* 3.6 22.7 - - + +
180B LEU* 4.7 9.4 - - + -
185B ILE* 5.2 2.0 - - + -
208B PHE* 4.2 12.3 - - + -
373B PRO* 3.9 23.3 - - + -
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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