Contacts of the helix formed by residues 87 - 105 (chain A) in PDB entry 1XGW
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 87 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ASP* 3.0 19.8 - - - +
83A ASP* 4.5 5.9 + - - -
84A ASN* 3.5 8.1 + - - +
85A LYS 3.5 1.4 - - - -
86A LYS* 1.3 103.0 - - - +
88A TRP* 1.3 64.2 + - - +
89A ARG 3.4 2.9 - - - -
90A ARG* 2.9 56.7 + - + +
91A VAL* 3.4 22.0 + - - +
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Residues in contact with TRP 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LYS 4.0 1.8 + - - -
87A ASN* 1.3 72.0 - - - +
89A ARG* 1.3 110.2 + - + +
91A VAL* 3.3 0.9 + - - -
92A TYR* 2.9 43.1 + + + -
126A TYR* 3.6 17.6 + - + +
128A PHE* 3.8 32.8 - + + -
130A ASP* 6.1 0.6 - - + +
136A GLN* 3.5 53.0 - - + +
139A ASN* 3.4 35.2 - - + -
140A ILE* 3.2 22.1 - - + +
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Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASN 4.6 0.2 - - - -
46A ASP* 3.8 23.1 - - + +
47A ASP 3.4 23.1 - - - +
48A PRO* 3.7 32.7 + - - +
49A TRP* 5.0 0.6 - - - +
50A GLY* 5.3 4.6 - - - +
87A ASN 3.4 0.4 - - - -
88A TRP* 1.3 120.3 - - + +
90A ARG* 1.3 60.9 + - - +
92A TYR* 3.1 25.5 + - - -
93A LYS* 2.9 51.4 + - + +
96A LEU* 6.0 0.4 - - - +
136A GLN* 5.3 1.0 - - - +
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 3.2 32.1 - - - +
45A ASN 4.5 1.0 + - - -
46A ASP* 4.1 15.1 + - - +
79A ARG* 3.4 61.8 - - - +
82A LYS 4.9 4.0 + - - -
83A ASP* 3.7 20.2 + - - +
84A ASN* 5.1 1.5 - - - +
87A ASN* 2.9 58.5 + - + +
89A ARG* 1.3 78.9 - - - +
91A VAL* 1.3 56.1 + - - +
93A LYS* 3.5 0.5 + - - -
94A SER* 2.7 32.6 + - - -
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG 4.4 3.8 - - - +
80A MET* 3.6 18.4 - - + +
84A ASN* 3.5 37.5 - - + +
87A ASN 3.4 12.8 + - - +
88A TRP 3.3 6.2 + - - +
89A ARG 3.3 0.2 - - - -
90A ARG* 1.3 76.4 - - + +
92A TYR* 1.3 63.4 + - - +
94A SER* 3.1 16.8 + - - -
95A LEU* 3.1 13.0 + - + +
123A LEU* 3.8 31.4 - - + -
126A TYR* 4.2 5.8 - - + +
140A ILE* 3.8 18.2 - - + -
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Residues in contact with TYR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TRP* 2.9 32.0 + + + +
89A ARG* 3.1 31.8 + - - +
91A VAL* 1.3 76.0 - - - +
93A LYS* 1.3 57.6 + - - +
95A LEU* 3.3 8.0 + - + +
96A LEU* 3.0 49.0 + - + +
139A ASN* 3.4 45.9 + - + +
140A ILE* 4.0 10.3 - - + +
143A LYS* 3.7 25.7 - - + +
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Residues in contact with LYS 93 (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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42A GLU 5.0 0.4 + - - -
43A ALA 3.4 24.4 - - - +
44A THR* 4.2 5.8 - - - +
45A ASN* 2.6 49.3 + - - +
47A ASP* 3.1 15.7 + - - +
49A TRP* 3.4 19.4 + - - -
50A GLY* 3.8 12.3 - - - -
51A PRO* 3.8 17.8 - - + +
89A ARG* 2.9 34.7 + - + +
90A ARG 3.9 3.8 - - - +
92A TYR* 1.3 76.4 - - + +
94A SER* 1.3 60.1 + - - +
95A LEU 3.2 0.4 - - - -
96A LEU* 3.5 11.2 - - + +
97A LEU* 2.8 28.9 + - - +
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Residues in contact with SER 94 (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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44A THR* 3.2 16.3 - - - +
76A LEU* 3.7 24.8 - - - +
79A ARG* 4.0 1.4 - - - +
80A MET* 3.7 35.3 + - - -
90A ARG 2.7 20.2 + - - -
91A VAL 3.1 8.7 + - - -
93A LYS* 1.3 76.8 - - - +
95A LEU* 1.3 59.3 + - - +
97A LEU* 4.4 0.4 - - - -
98A LEU* 2.8 31.0 + - - +
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Residues in contact with LEU 95 (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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80A MET* 4.0 6.3 - - + -
91A VAL 3.1 14.8 + - - +
92A TYR* 3.4 10.1 - - - +
94A SER* 1.3 74.9 - - - +
96A LEU* 1.3 55.0 + - - +
98A LEU* 3.3 0.6 + - - -
99A ALA* 2.8 37.3 + - - +
120A LEU* 3.7 30.1 - - + -
123A LEU* 3.9 14.4 - - + -
140A ILE* 3.8 40.8 - - + +
143A LYS* 3.8 26.2 - - + -
144A VAL* 3.9 11.7 - - + +
147A LEU* 3.8 15.1 - - + +
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Residues in contact with LEU 96 (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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50A GLY* 3.7 30.1 - - - -
51A PRO* 3.9 9.9 - - + -
56A MET* 4.2 6.8 - - - +
89A ARG* 6.0 0.4 - - - +
92A TYR* 3.0 38.9 + - + +
93A LYS* 3.5 15.5 - - + +
95A LEU* 1.3 76.5 - - - +
97A LEU* 1.3 60.8 + - - +
99A ALA* 3.5 3.1 + - - +
100A TYR* 3.1 22.7 + - - +
143A LYS* 3.2 32.1 - - - +
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Residues in contact with LEU 97 (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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40A VAL* 4.5 12.1 - - + -
43A ALA* 4.0 20.4 - - + -
44A THR* 4.7 2.5 - - + -
51A PRO* 4.7 4.7 - - + +
56A MET* 3.9 39.2 - - + -
59A ILE* 4.0 19.3 - - + -
76A LEU* 4.1 21.3 - - + -
93A LYS 2.8 20.0 + - - +
94A SER* 3.8 5.4 - - - +
96A LEU* 1.3 70.4 - - - +
98A LEU* 1.3 60.3 + - - +
100A TYR* 3.2 2.3 + - - +
101A LEU* 2.8 57.6 + - + +
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A MET* 4.9 5.8 - - - -
76A LEU* 4.1 23.1 - - + +
77A TRP* 4.2 17.7 - - + -
80A MET* 4.2 10.3 - - + -
94A SER 2.8 21.1 + - - +
95A LEU 3.9 2.7 - - - +
97A LEU* 1.3 70.4 - - - +
99A ALA* 1.3 65.2 + - - +
101A LEU* 4.4 1.8 - - + -
102A ILE* 2.9 26.9 + - + +
109A VAL* 3.9 24.9 - - + +
113A ALA* 4.6 15.9 - - + -
120A LEU* 4.0 24.2 - - + -
147A LEU* 3.8 24.0 - - + -
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Residues in contact with ALA 99 (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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95A LEU 2.8 22.0 + - - +
96A LEU 3.5 5.8 - - - +
98A LEU* 1.3 71.0 - - - +
100A TYR* 1.3 61.9 + - - +
102A ILE* 3.3 17.3 - - - +
103A ARG* 3.4 28.6 + - - +
143A LYS* 3.8 20.4 - - - +
147A LEU* 3.8 20.8 - - + +
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Residues in contact with TYR 100 (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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53A GLY* 3.9 8.7 + - - -
56A MET* 3.3 63.3 - - + -
57A GLY* 3.5 18.3 - - - -
60A ALA* 3.8 15.8 - - + +
96A LEU 3.1 11.1 + - - +
97A LEU 3.5 7.0 - - - +
99A ALA* 1.3 78.2 - - - +
101A LEU* 1.3 58.0 + - + +
103A ARG* 3.2 6.6 + - - +
104A ASN* 2.8 67.9 + - + +
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Residues in contact with LEU 101 (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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56A MET 4.2 1.6 - - - +
59A ILE* 3.9 18.6 - - + -
60A ALA* 3.5 39.5 - - + +
63A THR* 4.2 4.9 - - + -
72A LEU* 4.3 10.5 - - + -
73A MET* 4.5 7.2 - - + -
76A LEU* 4.0 18.8 - - + -
97A LEU* 2.8 48.3 + - + +
98A LEU* 3.3 3.6 + - - +
100A TYR* 1.3 71.8 - - + +
102A ILE* 1.3 62.4 + - - +
105A GLY* 2.7 31.9 + - - +
109A VAL* 3.6 20.0 - - + +
161A ARG* 3.8 0.5 + - - -
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Residues in contact with ILE 102 (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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98A LEU* 2.9 16.5 + - + +
99A ALA* 3.3 19.7 - - - +
101A LEU* 1.3 77.3 - - - +
103A ARG* 1.3 53.0 + - - +
109A VAL* 3.6 11.8 - - + +
110A VAL* 3.9 25.4 - - + +
113A ALA* 3.9 19.1 - - + -
114A ARG* 6.2 0.4 - - + +
147A LEU* 4.3 8.1 - - + -
150A PHE* 3.7 23.6 - - + -
151A ALA* 3.7 33.4 - - + -
157A LEU* 3.5 15.8 - - + +
161A ARG* 2.8 29.6 + - - +
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Residues in contact with ARG 103 (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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99A ALA* 3.4 34.4 + - - +
100A TYR* 3.2 10.4 + - - +
101A LEU 3.1 0.4 - - - -
102A ILE* 1.3 80.1 - - - +
104A ASN* 1.3 72.2 + - - +
105A GLY 3.8 0.2 - - - -
147A LEU* 5.1 1.0 - - - +
150A PHE* 3.4 50.5 - - + +
156A ARG* 4.4 10.9 - - - +
157A LEU* 5.1 0.2 - - - -
160A GLU* 2.7 42.3 + - + +
161A ARG* 4.1 30.3 + - - +
164A ALA* 4.5 4.5 - - - +
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Residues in contact with ASN 104 (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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60A ALA* 4.1 8.5 - - + +
64A PHE* 3.6 13.9 - - - -
100A TYR* 2.8 70.6 + - + +
103A ARG* 1.3 84.2 - - - +
105A GLY* 1.3 64.8 + - - +
164A ALA* 3.2 30.9 - - + +
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Residues in contact with GLY 105 (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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60A ALA* 3.7 11.9 - - - +
63A THR* 3.3 13.5 - - - -
64A PHE* 3.6 7.3 - - - -
101A LEU* 2.7 25.5 + - - +
104A ASN* 1.3 76.7 - - - +
106A SER* 1.3 62.2 + - - -
109A VAL* 4.5 1.8 - - - -
161A ARG* 2.5 29.3 + - - -
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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