Contacts of the helix formed by residues 110 - 129 (chain B) in PDB entry 1VYH
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 THR 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ASN* 1.3 76.4 - - - +
111B ALA* 1.3 67.7 + - - +
112B GLU* 3.0 21.8 + - - +
113B GLU* 2.9 40.2 + - + +
114B VAL* 3.0 11.8 + - - +
152B LYS* 5.0 1.8 - - - -
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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 ASN 3.8 1.2 + - - -
110B THR* 1.3 71.3 - - - +
112B GLU* 1.3 66.7 + - + +
114B VAL* 3.1 6.9 + - - +
115B ALA* 3.0 21.0 + - - +
152B LYS* 3.9 24.0 - - + +
155B LYS* 3.5 45.3 - - + -
156B VAL* 3.7 15.5 - - + +
159B LEU* 5.2 1.8 - - + -
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B THR* 3.0 24.9 + - - +
111B ALA* 1.3 81.4 - - + +
113B GLU* 1.3 64.5 + - + +
115B ALA* 3.0 6.9 + - - +
116B GLY* 3.0 17.7 + - - -
155B LYS* 4.1 19.5 - - + +
159B LEU* 4.0 26.6 - - + +
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Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASN* 3.0 36.5 - - + +
8B PRO* 3.5 18.3 - - - +
9B ALA* 3.6 4.6 - - + +
108B GLU 4.3 1.6 - - - +
109B ASN* 2.9 36.5 - - + +
110B THR* 2.9 28.2 + - + +
112B GLU* 1.3 77.5 - - + +
114B VAL* 1.3 58.7 + - - +
116B GLY* 2.9 3.9 + - - -
117B GLY 2.9 23.6 + - - -
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA* 4.2 6.0 - - - +
78B THR* 4.3 4.1 - - + +
103B GLY* 4.4 23.1 - - - +
106B ASN* 3.9 26.0 - - + +
109B ASN* 4.1 13.5 - - + +
110B THR 3.0 16.8 + - - +
111B ALA* 3.2 9.9 - - - +
113B GLU* 1.3 72.7 - - - +
115B ALA* 1.3 64.8 - - - +
117B GLY* 3.0 10.6 + - - +
118B ILE* 3.0 18.0 + - + +
139B LEU* 4.5 2.7 - - + -
152B LYS* 4.9 5.2 - - - -
156B VAL* 3.6 28.0 - - + -
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ALA 3.0 12.0 + - - +
112B GLU 3.3 9.2 - - - +
114B VAL* 1.3 78.0 - - - +
116B GLY* 1.3 63.5 + - - +
118B ILE* 3.4 7.2 + - - +
119B GLU* 2.9 42.8 + - - +
156B VAL* 4.6 9.2 - - + +
159B LEU* 4.0 26.5 - - + -
160B LEU* 4.2 8.9 - - + +
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Residues in contact with GLY 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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7B ASN* 4.1 8.5 - - - -
10B ALA* 4.4 3.7 - - - +
112B GLU 3.0 8.9 + - - -
113B GLU* 2.9 9.8 + - - -
115B ALA* 1.3 76.2 - - - +
117B GLY* 1.3 55.4 + - - +
119B GLU* 3.2 13.4 + - - +
120B ALA* 2.8 30.7 + - - +
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Residues in contact with GLY 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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7B ASN* 4.0 1.0 + - - -
9B ALA* 3.8 22.7 - - - -
10B ALA* 4.1 7.6 - - - -
78B THR* 4.0 12.1 - - - -
82B LEU* 4.4 0.7 - - - +
113B GLU 2.9 12.5 + - - -
114B VAL 3.0 4.6 + - - -
116B GLY* 1.3 72.4 - - - +
118B ILE* 1.3 63.8 + - - +
120B ALA* 3.0 6.6 + - - +
121B ILE* 3.0 23.6 + - - +
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Residues in contact with ILE 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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78B THR* 3.9 9.1 - - + +
100B VAL* 5.0 8.3 - - + -
102B VAL* 3.5 27.4 - - + +
114B VAL* 3.0 16.9 + - + +
115B ALA 3.7 4.9 - - - +
117B GLY* 1.3 71.6 - - - +
119B GLU* 1.3 57.7 + - - +
121B ILE* 2.9 14.8 + - + +
122B VAL* 2.8 33.4 + - + +
136B VAL* 4.2 29.8 - - + -
137B LEU 5.8 1.1 - - - +
139B LEU* 4.9 3.1 - - + -
156B VAL* 4.1 15.3 - - + -
160B LEU* 3.5 36.8 - - + -
164B LEU* 5.4 0.2 - - + -
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Residues in contact with GLU 119 (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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115B ALA* 2.9 39.0 + - - +
116B GLY* 3.4 8.9 - - - +
118B ILE* 1.3 75.0 - - - +
120B ALA* 1.3 57.7 + - - +
122B VAL* 3.2 11.3 + - - +
123B GLN* 2.8 36.1 + - - +
159B LEU* 4.5 1.6 - - - +
160B LEU* 3.6 13.4 - - + +
163B SER* 2.6 37.8 + - - +
164B LEU* 4.3 8.7 - - + -
167B LEU* 4.2 13.3 - - + +
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Residues in contact with ALA 120 (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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10B ALA* 3.8 22.7 - - + +
82B LEU* 4.3 13.5 - - + +
116B GLY 2.8 16.3 + - - +
117B GLY 3.3 9.2 - - - +
119B GLU* 1.3 68.2 - - - +
121B ILE* 1.3 61.3 + - - +
123B GLN* 3.3 18.5 - - - +
124B LEU* 2.9 29.5 + - - +
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B THR* 3.8 39.3 - - + +
81B VAL* 4.0 17.9 - - + -
82B LEU* 3.6 22.4 - - + -
85B LEU* 4.1 10.5 - - + +
100B VAL* 3.8 23.8 - - + -
102B VAL* 4.7 7.0 - - + -
117B GLY 3.0 17.4 + - - +
118B ILE* 2.9 11.8 + - - +
120B ALA* 1.3 72.2 - - - +
122B VAL* 1.3 65.9 + - + +
124B LEU* 3.1 6.9 + - - +
125B ILE* 2.9 43.7 + - + +
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B VAL* 5.4 0.7 - - + -
118B ILE* 2.8 25.8 + - + +
119B GLU* 3.4 8.5 - - - +
121B ILE* 1.3 75.8 - - + +
123B GLN* 1.3 63.7 + - - +
125B ILE* 3.0 10.9 + - - +
126B ASN* 3.0 32.4 + - - +
134B ILE* 3.8 9.2 - - + -
136B VAL* 4.0 27.4 - - + -
164B LEU* 4.4 7.9 - - + -
167B LEU* 4.4 9.4 - - + -
170B VAL* 3.5 39.0 - - + -
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Residues in contact with GLN 123 (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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119B GLU* 2.8 17.9 + - - +
120B ALA* 3.3 25.3 - - - +
122B VAL* 1.3 72.2 - - - +
124B LEU* 1.3 62.4 + - - +
126B ASN* 2.8 29.2 + - - +
127B THR* 3.1 13.1 + - - -
167B LEU* 3.9 22.3 - - + +
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Residues in contact with LEU 124 (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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82B LEU* 4.3 12.8 - - + +
85B LEU* 3.9 15.7 - - + -
86B LYS* 3.8 56.3 - - + +
90B LEU* 4.6 7.0 - - + -
120B ALA 2.9 13.1 + - - +
121B ILE* 3.4 9.9 - - - +
123B GLN* 1.3 74.0 - - - +
125B ILE* 1.3 65.7 + - + +
127B THR* 2.9 18.5 + - + +
128B ARG* 3.0 42.7 + - - +
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Residues in contact with ILE 125 (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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45B VAL* 4.9 1.8 - - + -
85B LEU* 4.1 16.4 - - + -
90B LEU* 4.4 14.6 - - + -
98B ILE* 3.6 34.5 - - + -
100B VAL* 3.6 21.1 - - + -
121B ILE* 2.9 43.0 + - + +
122B VAL* 3.4 8.1 - - - +
124B LEU* 1.3 75.8 - - - +
126B ASN* 1.3 55.5 + - - +
127B THR 3.0 0.7 + - - -
128B ARG 3.2 0.5 + - - -
129B GLN* 2.6 40.9 + - + +
132B ALA* 5.1 0.4 - - + -
134B ILE* 3.5 25.1 - - + -
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Residues in contact with ASN 126 (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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122B VAL* 3.0 31.3 + - - +
123B GLN* 2.8 30.7 + - - +
125B ILE* 1.3 76.5 - - - +
127B THR* 1.3 61.6 + - - +
129B GLN 4.1 11.0 - - - +
130B PRO* 3.6 19.3 - - + +
132B ALA 5.4 3.6 - - - +
134B ILE* 4.1 8.0 - - + +
167B LEU* 5.0 2.6 - - - +
168B ALA* 3.4 35.2 + - + +
169B ASN* 5.7 2.2 - - - +
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Residues in contact with THR 127 (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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123B GLN 3.1 12.5 + - - -
124B LEU* 2.9 15.3 + - + +
126B ASN* 1.3 80.1 + - - +
128B ARG* 1.3 84.9 + - - +
130B PRO* 3.3 12.8 - - - +
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Residues in contact with ARG 128 (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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85B LEU 4.7 3.4 + - - -
86B LYS* 3.3 46.8 + - - +
90B LEU* 4.2 34.3 - - + +
91B GLU* 5.2 11.4 + - - +
94B LYS* 5.3 6.8 + - - -
124B LEU* 3.0 38.0 + - - +
125B ILE 4.3 0.2 - - - +
127B THR* 1.3 89.1 - - - +
129B GLN* 1.3 68.0 + - + +
130B PRO* 3.4 5.6 - - - +
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Residues in contact with GLN 129 (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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90B LEU* 2.5 61.6 + - + +
93B ILE* 3.4 24.0 + - - +
94B LYS* 3.7 3.7 + - - +
95B PRO* 3.4 9.8 - - - +
98B ILE* 4.3 7.2 - - + -
125B ILE* 2.6 24.5 + - - +
126B ASN* 4.1 3.7 - - - -
128B ARG* 1.3 79.9 + - + +
130B PRO* 1.3 65.7 - - - +
131B GLN* 2.9 34.7 + - - +
132B ALA* 2.9 23.6 + - + +
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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