Contacts of the helix formed by residues 111 - 129 (chain A) in PDB entry 3VA2
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 ARG 111 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ARG* 1.3 80.6 - - - +
112A VAL* 1.3 65.5 + - - +
113A ASN* 3.3 26.1 - - - +
114A GLN* 3.1 17.9 + - - +
115A PHE* 3.1 9.9 + - - +
48B GLU* 6.3 1.6 - - - -
50B LEU 4.0 2.7 - - - -
51B ARG* 3.4 29.4 - - - +
74C GLU* 3.9 16.6 + - - +
75C ASP* 3.6 29.4 + - - +
76C ASP* 3.1 38.4 + - - +
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG 4.6 0.2 - - - -
111A ARG* 1.3 73.0 - - - +
113A ASN* 1.3 57.7 + - - +
115A PHE* 3.1 8.5 + - + +
116A LEU* 2.9 48.3 + - + +
44B LEU 3.6 23.1 - - - +
45B ILE* 3.9 6.1 - - + -
47B ASN* 3.8 22.2 + - + +
50B LEU* 4.0 24.1 + - + +
52B ILE* 4.0 19.7 - - + -
74B LEU* 4.0 18.4 - - + -
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Residues in contact with ASN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ARG* 3.3 27.3 - - - +
112A VAL* 1.3 79.2 + - - +
114A GLN* 1.3 85.6 + - - +
116A LEU* 3.8 1.7 + - - -
117A ASP* 3.1 31.7 + - - +
41B ARG* 3.5 16.3 + - - +
45B ILE* 3.6 33.4 - - + +
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Residues in contact with GLN 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG* 3.3 46.1 + - + +
111A ARG* 3.1 16.3 + - + +
113A ASN* 1.3 92.2 - - - +
115A PHE* 1.3 66.5 + - - +
117A ASP* 3.5 11.0 - - - +
118A TYR* 3.3 19.6 + - - +
54B VAL* 4.2 7.5 - - + +
75C ASP* 3.3 29.7 + - - +
76C ASP 5.2 0.2 - - - +
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Residues in contact with PHE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ARG 3.1 8.9 + - - +
112A VAL* 3.1 9.5 + - - +
114A GLN* 1.3 75.8 - - - +
116A LEU* 1.3 79.7 + - + +
118A TYR* 3.0 9.8 + + + +
119A LEU* 2.9 31.2 + - + +
52B ILE* 3.4 37.5 - - + -
53B PRO 3.6 17.9 - - - -
54B VAL* 3.6 16.9 - - + +
55B PRO* 6.0 1.3 - - + -
67B ILE* 3.2 42.8 - - + -
70B GLY* 3.7 7.9 - - - -
71B ILE* 3.7 26.2 - - + -
74B LEU* 4.5 6.5 - - + -
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A VAL* 2.9 19.9 + - + +
113A ASN 4.0 0.7 - - - +
115A PHE* 1.3 83.0 - - + +
117A ASP* 1.3 61.5 + - - +
119A LEU* 3.7 8.6 - - + +
120A GLN* 2.8 33.3 + - - +
37B LEU* 4.1 26.6 - - + +
41B ARG* 3.9 25.4 - - + +
44B LEU* 3.9 24.9 - - + -
45B ILE* 3.7 27.6 - - + -
74B LEU* 3.7 25.4 - - + -
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Residues in contact with ASP 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ASN* 3.2 12.6 + - - +
114A GLN* 3.5 15.4 - - - +
116A LEU* 1.3 79.0 - - - +
118A TYR* 1.3 55.2 + - - +
120A GLN* 3.8 11.8 - - - +
121A GLU* 3.0 33.2 + - - +
41B ARG* 2.8 36.1 + - - -
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Residues in contact with TYR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLN 3.3 9.2 + - - +
115A PHE* 3.0 11.7 + + + +
117A ASP* 1.3 78.4 - - - +
119A LEU* 1.3 55.3 + - - +
121A GLU* 3.2 6.6 + - + +
122A PHE* 2.6 35.3 + - - +
54B VAL* 4.1 18.4 - - + -
55B PRO* 3.4 42.6 - - + +
57B HIS* 2.8 28.6 + - - -
58B LYS* 4.2 15.0 - - + -
59B ASN 4.1 2.3 + - - -
60B HIS* 3.4 46.2 + + - -
63B CYS* 4.5 0.5 - - - -
67B ILE* 3.9 25.4 - - + -
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PHE* 2.9 29.9 + - + +
116A LEU* 3.7 15.5 - - + +
118A TYR* 1.3 78.1 - - - +
120A GLN* 1.3 56.6 + - - +
122A PHE* 3.2 17.6 + - + +
123A LEU* 2.9 37.8 + - + +
37B LEU* 3.8 26.5 - - + -
67B ILE* 3.7 27.4 - - + -
68B PHE* 5.6 0.7 - - + -
71B ILE* 3.8 28.0 - - + -
74B LEU* 6.2 0.4 - - + -
91B LEU* 4.3 11.2 - - + -
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Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU 2.8 18.3 + - - +
117A ASP* 3.8 15.2 - - - +
119A LEU* 1.3 77.3 - - - +
121A GLU* 1.3 62.7 + - - +
123A LEU* 3.5 2.8 + - - +
124A GLY* 3.1 20.1 + - - -
34B LEU* 3.8 31.6 - - + +
37B LEU* 5.0 7.4 - - + +
38B SER* 6.3 1.0 - - - -
41B ARG* 4.6 6.1 + - - -
314C SER 5.6 2.2 + - - -
317C ARG 5.4 1.0 + - - -
318C GLU* 2.7 45.0 + - - +
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Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASP* 3.0 22.5 + - - +
118A TYR* 3.5 8.2 - - - +
120A GLN* 1.3 76.2 - - - +
122A PHE* 1.3 63.6 + - - +
124A GLY* 3.4 2.3 + - - -
125A VAL* 3.2 27.7 + - - +
58B LYS* 3.3 27.3 + - - +
60B HIS* 3.5 16.5 + - + +
208C ARG* 3.1 44.7 + - + +
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Residues in contact with PHE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A TYR 2.6 17.3 + - - +
119A LEU* 3.2 20.2 + - + +
121A GLU* 1.3 74.4 - - - +
123A LEU* 1.3 80.3 + - + +
125A VAL* 3.1 15.1 + - - +
126A MET* 3.3 44.2 + - + +
60B HIS* 3.6 36.1 - - + -
61B GLN* 4.5 7.9 - - + -
64B THR* 4.1 13.7 - - + -
67B ILE* 3.6 28.3 - - + -
68B PHE* 4.1 18.6 - + - -
98B ILE* 3.7 17.0 - - + -
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Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 2.9 22.1 + - + +
122A PHE* 1.3 97.8 - - + +
124A GLY* 1.3 61.0 + - - +
126A MET* 3.6 15.1 + - - +
127A ASN* 3.3 22.0 + - - +
30B VAL* 3.6 29.8 - - + +
33B THR* 4.2 22.0 - - + -
34B LEU* 3.6 30.5 - - + -
37B LEU* 4.2 10.3 - - + -
68B PHE* 5.7 0.2 - - + -
91B LEU* 4.3 10.8 - - + -
94B ILE* 3.9 19.1 - - + -
315C MET 4.2 0.2 - - - +
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Residues in contact with GLY 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLN 3.1 14.3 + - - -
121A GLU* 3.4 4.9 + - - -
122A PHE 3.1 0.4 - - - -
123A LEU* 1.3 77.8 - - - +
125A VAL* 1.3 51.3 + - - +
127A ASN* 3.6 0.7 + - - +
128A THR* 2.5 36.7 + - - -
34B LEU* 4.4 3.3 - - - +
208C ARG* 3.5 1.1 - - - -
315C MET 3.4 13.0 - - - -
316C CYS* 3.3 23.6 - - - +
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLU 3.2 15.7 + - - +
122A PHE 3.1 8.2 + - - +
124A GLY* 1.3 74.3 - - - +
126A MET* 1.3 54.6 + - - +
128A THR* 3.1 1.7 + - - -
129A GLU* 2.7 45.4 + - + +
60B HIS* 3.5 26.2 - - + +
61B GLN* 3.8 28.5 - - + +
208C ARG* 3.4 30.3 - - - +
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Residues in contact with MET 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A PHE* 3.3 46.5 + - + +
123A LEU* 3.7 19.3 - - + +
125A VAL* 1.3 81.0 - - - +
127A ASN* 1.3 62.9 + - - +
129A GLU* 3.3 7.6 - - - +
130A TRP* 3.2 24.0 - - - +
30B VAL* 4.8 13.5 - - + -
61B GLN* 5.5 11.0 - - + +
94B ILE* 4.3 16.2 - - + -
97B TYR* 4.2 26.0 - - + -
98B ILE* 4.1 11.4 - - + -
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Residues in contact with ASN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU 3.3 5.4 + - - +
124A GLY 3.7 0.4 - - - +
125A VAL 3.2 0.4 - - - -
126A MET* 1.3 78.6 - - - +
128A THR* 1.3 55.6 + - - +
129A GLU 3.4 0.3 + - - -
130A TRP* 3.8 11.5 + - - +
27B SER 4.7 10.5 + - - +
30B VAL* 3.2 36.6 - - - +
31B LYS* 4.7 1.6 + - - +
268C HIS* 2.3 49.0 + - - -
269C CYS* 4.4 0.7 - - - -
315C MET* 3.2 47.2 - - - +
316C CYS* 4.8 1.9 - - - -
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Residues in contact with THR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A GLY 2.5 24.1 + - - -
125A VAL* 3.1 5.1 + - - -
127A ASN* 1.3 77.3 - - - +
129A GLU* 1.3 70.0 + - - +
130A TRP 3.5 3.5 + - - -
206C LYS* 4.0 15.7 + - + +
208C ARG* 2.9 19.6 + - - +
265C PHE* 3.9 27.1 - - + -
266C PRO* 3.8 17.0 - - + +
268C HIS* 3.6 12.5 - - - -
269C CYS* 3.8 8.9 - - - -
316C CYS* 3.2 9.9 - - - +
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Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASN* 4.1 18.4 + - - +
125A VAL* 2.7 35.7 + - + +
126A MET* 3.3 6.0 - - - +
128A THR* 1.3 78.9 - - - +
130A TRP* 1.3 63.8 + - - +
61B GLN* 4.6 13.1 + - - +
129B GLU* 4.6 18.7 - - - +
206C LYS* 2.6 37.3 + - - -
208C ARG* 5.3 3.2 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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