Contacts of the strand formed by residues 84 - 98 (chain S) in PDB entry 1H2I
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 TRP 84 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26S PHE* 3.8 5.6 - - - -
72S ILE* 4.2 12.3 - - + -
75S ALA* 3.5 30.1 - - + -
76S ASN* 2.7 25.5 + - - +
79S PHE* 3.9 19.1 - + + -
80S GLY 3.6 15.7 - - - -
81S TYR 4.2 6.1 + - - +
82S ASN 3.6 1.1 - - - -
83S GLY* 1.3 78.3 + - - +
85S ALA* 1.3 78.4 + - - +
86S HIS* 3.8 11.9 - + + -
113S VAL* 4.1 11.2 - - + -
114S GLN 3.1 10.1 - - - +
115S LEU* 4.0 7.4 - - + -
151S LEU* 3.9 28.0 - - + -
155S LEU* 4.2 9.9 - - + -
119T SER* 4.7 2.9 - - - -
120T TYR 4.3 0.2 - - - +
121T HIS* 3.3 44.3 + + - -
157T SER* 3.8 19.1 - - - -
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Residues in contact with ALA 85 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26S PHE* 3.7 11.2 - - + -
84S TRP* 1.3 80.8 - - - +
86S HIS* 1.3 55.9 + - - +
113S VAL* 3.1 8.5 - - - +
114S GLN 2.7 31.1 + - - +
120T TYR* 2.7 58.3 - - + +
121T HIS* 3.9 3.8 - - - -
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Residues in contact with HIS 86 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84S TRP* 3.8 4.8 - + + -
85S ALA* 1.3 77.9 - - - +
87S SER* 1.3 64.6 + - - +
88S ILE* 5.5 0.4 - - + -
111S VAL* 4.0 19.1 - - + -
112S ARG 3.0 12.1 - - - +
113S VAL* 4.0 4.3 - - + -
147S VAL* 5.1 6.4 - - + +
151S LEU* 3.8 39.3 - - + +
120T TYR* 3.2 12.3 + - - -
121T HIS* 2.8 47.0 - + + -
122T GLU 3.0 49.4 + - - -
123T ASP* 5.1 5.2 + - - -
157T SER* 3.5 18.4 - - - -
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Residues in contact with SER 87 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86S HIS* 1.3 78.1 - - - +
88S ILE* 1.3 65.2 + - - +
89S THR* 4.6 7.1 - - - +
111S VAL* 3.4 7.1 - - - +
112S ARG* 2.8 46.5 + - - +
112T ARG* 5.2 6.7 - - - -
120T TYR* 3.9 17.5 + - - -
122T GLU* 3.4 16.4 - - - -
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Residues in contact with ILE 88 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86S HIS* 5.5 1.1 - - + -
87S SER* 1.3 75.7 - - - +
89S THR* 1.3 62.8 + - - +
90S GLN* 3.6 28.2 - - - +
91S GLN* 4.1 5.4 - - + +
109S ALA* 5.1 3.1 - - + -
110S PHE 3.5 7.4 - - - +
111S VAL* 4.6 6.3 - - + -
147S VAL* 3.8 26.7 - - + -
110T PHE* 3.8 33.0 - - + -
122T GLU* 2.8 30.7 + - + +
123T ASP* 3.8 29.4 - - - +
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Residues in contact with THR 89 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87S SER* 3.6 6.4 + - - +
88S ILE* 1.3 73.9 - - - +
90S GLN* 1.3 64.4 + - - +
110S PHE* 2.8 22.7 + - - +
112S ARG* 4.0 27.1 - - + -
122S GLU* 2.7 29.5 + - - +
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Residues in contact with GLN 90 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88S ILE* 3.1 9.6 - - - +
89S THR* 1.3 86.7 + - - +
91S GLN* 1.3 64.3 + - - +
92S ASN* 3.7 33.5 - - - +
109S ALA* 3.5 1.4 - - - -
110S PHE* 2.7 52.6 + - + -
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Residues in contact with GLN 91 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88S ILE* 4.1 4.4 - - + +
90S GLN* 1.3 81.0 - - - +
92S ASN* 1.3 65.6 + - - +
93S VAL 4.2 0.9 + - - -
107S VAL* 3.7 17.8 - - + +
108S CYS 3.4 11.7 - - - +
109S ALA* 4.0 1.4 - - - +
143S ARG* 2.9 71.0 + - - +
146S ALA* 3.9 5.3 - - - +
147S VAL* 3.5 16.2 - - - +
110T PHE* 3.3 35.5 - - + -
124T VAL* 3.9 1.2 - - - +
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Residues in contact with ASN 92 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143R ARG* 4.9 3.7 + - - +
90S GLN* 3.7 23.3 - - - +
91S GLN* 1.3 75.7 + - - +
93S VAL* 1.3 76.2 + - - +
94S ASP* 3.3 14.4 + - - +
107S VAL* 3.6 2.6 - - - -
108S CYS* 2.8 50.7 + - - -
110S PHE* 5.5 0.4 - - + -
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Residues in contact with VAL 93 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91S GLN 4.2 0.4 + - - -
92S ASN* 1.3 80.5 + - - +
94S ASP* 1.3 61.7 + - - +
95S PHE* 3.8 14.1 - - - +
96S VAL* 3.9 24.5 - - + -
105S VAL* 4.8 0.2 - - + -
106S GLY 4.0 6.1 - - - +
107S VAL* 3.8 18.4 - - + -
139S LEU* 4.4 8.3 - - + -
143S ARG* 3.5 37.4 - - - +
94T ASP* 5.8 0.4 - - - -
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Residues in contact with ASP 94 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93R VAL* 5.7 0.4 - - - -
139R LEU* 3.5 15.0 - - + +
143R ARG* 2.5 34.2 + - - -
92S ASN* 3.3 17.6 + - - +
93S VAL* 1.3 73.6 - - - +
95S PHE* 1.3 73.6 + - + +
106S GLY 2.9 14.5 + - - +
108S CYS* 4.7 0.2 - - - -
126S TYR* 2.6 33.6 + - - +
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Residues in contact with PHE 95 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135R LYS* 3.7 42.0 - - + +
136R ALA* 3.5 33.2 - - + -
139R LEU* 3.9 14.1 - - + -
93S VAL* 3.4 4.6 - - - +
94S ASP* 1.3 89.9 - - + +
96S VAL* 1.3 68.6 + - - +
97S ASP* 3.6 19.3 - - - +
104S TYR* 3.2 34.8 - - + -
105S VAL* 3.4 5.6 - - - +
106S GLY* 3.2 37.4 + - - +
126S TYR* 4.0 0.7 - - - -
130S GLU* 5.8 0.4 - - - -
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Residues in contact with VAL 96 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93S VAL* 3.9 17.5 - - + -
95S PHE* 1.3 79.7 - - - +
97S ASP* 1.3 65.6 + - - +
98S LEU 4.3 0.3 + - - -
103S PHE* 4.1 22.2 - - + -
104S TYR 3.6 3.4 - - - -
105S VAL* 4.2 11.9 - - + -
135S LYS* 4.4 23.3 - - + -
139S LEU* 4.0 23.1 - - + -
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Residues in contact with ASP 97 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135R LYS* 2.8 35.5 + - - +
95S PHE* 3.6 12.8 - - - +
96S VAL* 1.3 81.3 + - - +
98S LEU* 1.3 59.2 + - - +
99S ASN* 3.9 18.7 - - - +
103S PHE* 3.2 8.6 - - - -
104S TYR* 2.6 52.1 + - + +
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Residues in contact with LEU 98 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96S VAL 4.3 0.6 + - - -
97S ASP* 1.3 72.0 - - - +
99S ASN* 1.3 67.7 + - - +
100S ASN 3.9 19.5 - - - +
101S GLY* 4.0 12.3 - - - +
102S LYS 3.3 12.8 - - - +
103S PHE* 3.8 34.3 - - + -
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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
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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