Contacts of the helix formed by residues 80 - 98 (chain A) in PDB entry 4X2Q
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 ASP 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A ARG 3.4 6.4 + - - +
79A MET* 1.3 77.2 - - - +
81A ALA* 1.3 65.5 + - - +
82A SER* 4.1 15.9 - - - +
83A GLU* 2.9 30.8 + - + +
84A ARG* 3.3 7.6 + - - +
127C LYS* 5.7 2.3 + - - -
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Residues in contact with ALA 81 (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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79A MET 3.5 2.4 + - - -
80A ASP* 1.3 71.1 - - - +
82A SER* 1.3 61.3 + - - +
84A ARG* 3.1 35.7 + - - +
136A ALA* 3.1 43.6 - - - +
137A ASP* 3.9 11.2 - - + -
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Residues in contact with SER 82 (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 ASP* 4.1 11.3 - - - +
81A ALA* 1.3 77.7 - - - +
83A GLU* 1.3 59.7 + - - +
85A GLY* 3.3 4.7 + - - +
86A ARG* 3.1 27.1 + - - +
136A ALA* 5.0 0.7 - - - -
137A ASP* 3.4 34.1 - - - +
127C LYS* 5.0 15.9 - - - +
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Residues in contact with GLU 83 (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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79A MET* 3.8 24.6 - - + +
80A ASP* 2.9 29.8 + - + +
82A SER* 1.3 76.9 + - - +
84A ARG* 1.3 61.0 + - - +
85A GLY 3.2 0.9 - - - -
86A ARG* 3.3 20.4 + - + +
87A LEU* 3.2 29.5 + - + +
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Residues in contact with ARG 84 (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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76A TRP* 3.9 37.3 + - + -
79A MET* 3.9 26.9 + - + -
80A ASP 3.3 7.0 + - - +
81A ALA* 3.1 35.3 + - - +
83A GLU* 1.3 76.0 - - - +
85A GLY* 1.3 60.9 + - - +
87A LEU* 3.6 4.9 + - - +
88A LEU* 3.3 28.0 + - - +
136A ALA* 4.2 10.8 + - + +
139A ILE* 5.2 1.2 - - - +
158A PRO* 5.8 3.2 - - - +
183A LEU 3.8 14.1 - - - +
184A CYS* 2.6 36.7 + - - -
185A CYS 3.6 5.7 + - - -
186A GLY* 3.4 16.5 - - - +
213A PHE* 5.4 0.2 - - - -
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Residues in contact with GLY 85 (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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81A ALA 3.2 9.5 + - - -
82A SER 3.3 7.5 + - - -
83A GLU 3.2 0.4 - - - -
84A ARG* 1.3 78.6 - - - +
86A ARG* 1.3 56.6 + - - +
88A LEU 3.4 0.2 + - - -
89A ASP* 3.0 26.5 + - - +
133A ALA* 3.2 38.1 - - - +
136A ALA* 3.5 6.7 - - - +
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Residues in contact with ARG 86 (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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82A SER* 3.1 19.5 + - - +
83A GLU* 3.4 24.2 - - + +
84A ARG 3.3 0.4 - - - -
85A GLY* 1.3 78.5 - - - +
87A LEU* 1.3 56.4 + - + +
89A ASP* 3.5 31.7 + - - +
90A LYS* 3.0 50.8 + - - +
93A ASP* 5.2 3.4 + - - -
93C ASP* 5.7 1.0 + - - -
130C ARG* 3.2 50.9 - - - +
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Residues in contact with LEU 87 (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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76A TRP* 4.0 6.7 - - + -
79A MET* 3.8 35.4 - - + -
83A GLU* 3.2 13.9 + - + +
84A ARG* 4.1 3.8 - - - +
85A GLY 3.3 0.2 - - - -
86A ARG* 1.3 75.2 - - + +
88A LEU* 1.3 60.9 + - - +
90A LYS* 3.9 5.0 - - + +
91A LEU* 3.1 27.2 + - - +
211A ALA* 3.4 29.9 - - + +
212A GLY* 3.5 24.9 - - - +
213A PHE* 3.5 34.7 - - + +
214A PRO* 4.3 1.6 - - + -
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Residues in contact with LEU 88 (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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76A TRP* 6.6 0.2 - - + -
84A ARG 3.3 22.6 + - - +
85A GLY* 4.8 0.4 - - - -
87A LEU* 1.3 76.8 - - - +
89A ASP* 1.3 60.9 + - - +
91A LEU* 3.3 9.5 + - + +
92A ALA 3.2 17.2 + - - -
129A PHE* 3.6 48.1 - - + +
132A TYR 3.6 26.5 - - - +
133A ALA* 3.7 13.2 - - + -
136A ALA* 5.4 0.4 - - + -
180A ALA* 3.9 26.7 - - + +
183A LEU* 4.5 17.7 - - + -
184A CYS* 4.0 15.3 - - - +
213A PHE* 4.6 4.0 - - + -
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Residues in contact with ASP 89 (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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85A GLY 3.0 18.0 + - - +
86A ARG* 3.6 24.8 + - - +
88A LEU* 1.3 75.6 - - - +
90A LYS* 1.3 62.0 + - - +
92A ALA* 3.5 5.9 + - - +
93A ASP* 3.2 26.8 + - - +
129A PHE 4.4 1.3 - - - -
130A ARG* 3.0 38.1 + - - +
133A ALA* 3.7 9.8 - - + +
86C ARG* 4.8 0.5 + - - -
89C ASP* 2.9 25.1 - - - +
130C ARG* 5.5 0.5 - - - -
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Residues in contact with LYS 90 (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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86A ARG* 3.0 40.5 + - - +
87A LEU* 3.9 8.1 - - + +
88A LEU 3.3 0.2 - - - -
89A ASP* 1.3 74.4 - - - +
91A LEU* 1.3 64.6 + - - +
93A ASP* 3.3 31.7 + - + +
94A LEU* 3.3 16.6 + - + +
211A ALA* 4.1 28.3 - - + +
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Residues in contact with LEU 91 (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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87A LEU 3.1 17.2 + - - +
88A LEU* 3.4 8.5 - - + +
89A ASP 3.3 0.2 - - - -
90A LYS* 1.3 76.2 - - - +
92A ALA* 1.3 64.3 + - - +
94A LEU* 3.2 7.6 + - - +
95A VAL* 3.1 26.4 + - - +
129A PHE* 3.7 33.7 - - + -
179A ILE* 5.2 5.6 - - + -
183A LEU* 5.4 0.2 - - + -
204A MET* 3.7 25.4 - - + -
207A LEU* 3.9 34.1 - - + +
208A ILE* 4.3 10.5 - - + +
211A ALA* 4.5 1.3 - - - +
213A PHE* 3.8 25.4 - - + -
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Residues in contact with ALA 92 (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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88A LEU 3.2 5.0 + - - +
89A ASP 3.5 5.6 - - - +
90A LYS 3.3 0.2 - - - -
91A LEU* 1.3 79.1 - - - +
93A ASP* 1.3 56.6 + - - +
95A VAL* 3.3 8.3 + - - +
96A GLU* 2.9 29.1 + - - +
126A ILE* 4.0 11.3 - - + +
129A PHE* 3.8 25.5 - - + +
130A ARG* 3.5 37.6 + - + +
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Residues in contact with ASP 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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86A ARG* 5.2 2.8 + - - -
89A ASP* 3.2 15.5 + - - +
90A LYS* 3.3 29.2 + - + +
91A LEU 3.2 0.2 - - - -
92A ALA* 1.3 77.9 - - - +
94A LEU* 1.3 54.1 + - + +
96A GLU* 3.1 6.7 + - - +
97A ARG* 2.8 35.3 + - - +
130A ARG* 2.8 24.7 + - - +
86C ARG* 5.6 1.4 + - - -
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Residues in contact with LEU 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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90A LYS* 3.3 16.1 + - + +
91A LEU* 3.2 8.6 + - - +
93A ASP* 1.3 78.5 - - + +
95A VAL* 1.3 60.2 + - - +
97A ARG* 3.5 32.8 + - - +
98A ASP* 3.0 35.3 + - - +
207A LEU* 3.3 48.9 - - + +
210A GLU* 3.5 18.8 - - + +
211A ALA* 3.7 25.8 - - + +
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Residues in contact with VAL 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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91A LEU 3.1 16.5 + - - +
92A ALA* 3.7 8.3 - - - +
93A ASP 3.3 0.2 - - - -
94A LEU* 1.3 76.3 - - - +
96A GLU* 1.3 56.7 + - - +
98A ASP 3.2 1.2 - - - -
99A ARG* 2.9 32.1 + - - +
102A LEU* 4.0 9.9 - - + -
122A LEU* 3.9 20.0 - - + -
125A VAL* 4.0 18.2 - - + -
126A ILE* 3.8 20.9 - - + -
129A PHE* 4.7 3.4 - - + -
172A LEU* 5.2 0.9 - - + -
204A MET* 3.8 33.2 - - + -
207A LEU* 3.9 8.5 - - + -
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Residues in contact with GLU 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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92A ALA 2.9 14.3 + - - +
93A ASP* 3.3 12.6 - - - +
95A VAL* 1.3 77.0 - - - +
97A ARG* 1.3 61.7 + - - +
99A ARG* 3.3 43.7 + - - +
126A ILE* 3.8 27.8 - - + +
130A ARG* 4.5 10.7 + - - +
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Residues in contact with ARG 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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93A ASP 2.8 18.7 + - - +
94A LEU* 3.5 21.3 + - - +
96A GLU* 1.3 75.2 - - - +
98A ASP* 1.3 92.6 + - - +
99A ARG 3.3 2.1 + - - -
100A ALA* 5.1 1.0 + - - +
101A VAL* 5.5 0.2 - - - +
203A TYR* 4.9 0.2 + - - -
207A LEU* 3.6 5.9 - - - +
210A GLU* 3.0 39.8 + - - -
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Residues in contact with ASP 98 (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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94A LEU 3.0 11.2 + - - +
95A VAL 3.2 4.5 - - - -
97A ARG* 1.3 124.0 + - - +
99A ARG* 1.3 57.1 + - - +
100A ALA 3.3 2.9 - - - -
101A VAL* 3.3 17.8 + - + +
102A LEU* 3.0 32.3 + - + +
203A TYR* 2.6 39.1 + - + +
207A LEU* 3.6 4.7 - - - +
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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