Contacts of the strand formed by residues 84 - 98 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119L SER* 4.7 2.8 - - - -
121L HIS* 3.3 40.3 + + - -
157L SER* 3.8 21.5 - - - -
26V PHE* 3.9 4.9 - - - -
72V ILE* 4.2 12.1 - - + -
75V ALA* 3.5 29.8 - - + -
76V ASN* 2.8 26.7 + - - +
79V PHE* 3.9 11.9 - + + -
80V GLY 3.5 15.7 - - - -
81V TYR 4.2 6.1 + - - +
82V ASN 3.6 0.7 - - - -
83V GLY* 1.3 78.8 + - - +
85V ALA* 1.3 80.5 + - - +
86V HIS* 3.7 16.8 - + - -
113V VAL* 4.1 10.8 - - + -
114V GLN 3.1 11.7 - - - +
115V LEU* 3.8 14.6 - - + -
151V LEU* 3.9 26.0 - - + -
155V LEU* 4.2 8.3 - - + -
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Residues in contact with ALA 85 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120L TYR* 2.8 57.2 - - + +
121L HIS* 3.8 4.5 - - - -
26V PHE* 3.7 11.7 - - + -
84V TRP* 1.3 80.5 - - - +
86V HIS* 1.3 58.3 + - - +
113V VAL* 3.1 8.5 - - - +
114V GLN 2.7 30.8 + - - +
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Residues in contact with HIS 86 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120L TYR* 3.1 12.5 + - - -
121L HIS* 2.8 47.3 - + + -
122L GLU 3.0 48.0 + - - -
123L ASP* 4.9 5.8 + - - -
157L SER* 3.5 18.4 - - - -
84V TRP* 3.7 4.5 - + + -
85V ALA* 1.3 79.9 - - - +
87V SER* 1.3 61.5 - - - +
88V ILE* 5.4 0.4 - - + -
111V VAL* 3.9 19.5 - - + -
112V ARG 3.1 12.6 - - - +
113V VAL* 4.0 3.8 - - + -
147V VAL* 5.1 6.1 - - + +
151V LEU* 3.8 39.6 - - + +
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Residues in contact with SER 87 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L ARG* 5.1 6.3 - - - -
120L TYR* 3.9 18.4 + - - -
122L GLU* 3.4 17.7 - - - -
86V HIS* 1.3 76.2 - - - +
88V ILE* 1.3 66.2 + - - +
89V THR* 3.6 6.6 + - - +
111V VAL* 3.4 7.2 - - - +
112V ARG* 2.9 44.3 + - - +
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Residues in contact with ILE 88 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110L PHE* 3.8 26.0 - - + -
122L GLU* 2.9 33.3 + - + +
123L ASP* 3.6 37.5 - - - -
86V HIS* 5.4 0.7 - - + -
87V SER* 1.3 75.2 - - - +
89V THR* 1.3 62.8 + - - +
90V GLN* 3.7 27.5 - - - +
91V GLN* 4.2 4.9 - - + +
109V ALA* 5.1 4.3 - - + -
110V PHE 3.5 6.3 - - - +
111V VAL* 4.7 6.1 - - + -
147V VAL* 3.9 26.2 - - + -
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Residues in contact with THR 89 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87V SER* 3.6 6.0 + - - +
88V ILE* 1.3 72.8 - - - +
90V GLN* 1.3 64.0 + - - +
110V PHE* 2.8 22.4 + - - +
112V ARG* 3.9 28.0 - - + -
122V GLU* 2.7 31.1 + - - +
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Residues in contact with GLN 90 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88V ILE* 3.1 9.4 - - - +
89V THR* 1.3 87.1 + - - +
91V GLN* 1.3 65.7 + - - +
92V ASN* 3.7 34.1 - - - +
109V ALA* 3.4 1.7 - - - -
110V PHE* 2.7 50.3 + - + -
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Residues in contact with GLN 91 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110L PHE* 3.3 35.4 - - + -
124L VAL* 3.8 0.9 - - - +
88V ILE* 4.2 5.1 - - + +
90V GLN* 1.3 82.1 + - - +
92V ASN* 1.3 63.5 + - - +
93V VAL 4.3 0.2 + - - -
107V VAL* 3.7 17.3 - - + +
108V CYS 3.3 14.1 - - - +
109V ALA* 4.0 1.7 - - + +
143V ARG* 2.9 69.8 + - - +
146V ALA* 3.9 5.1 - - - +
147V VAL* 3.4 17.4 - - - +
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Residues in contact with ASN 92 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143U ARG* 4.9 3.5 + - - +
90V GLN* 3.7 23.4 - - - +
91V GLN* 1.3 75.4 + - - +
93V VAL* 1.3 77.8 + - - +
94V ASP* 3.4 14.4 + - - +
107V VAL* 4.2 2.5 - - - -
108V CYS* 2.8 50.8 + - - -
110V PHE* 5.7 0.2 - - - -
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Residues in contact with VAL 93 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94L ASP* 5.4 0.4 - - - +
91V GLN 4.3 0.6 + - - -
92V ASN* 1.3 80.2 + - - +
94V ASP* 1.3 63.4 + - - +
95V PHE* 3.9 10.3 - - - +
96V VAL* 3.8 28.0 - - + -
107V VAL* 3.8 24.9 - - + -
139V LEU* 4.4 7.2 - - + -
143V ARG* 3.6 38.8 - - - +
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Residues in contact with ASP 94 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93U VAL* 5.3 1.0 - - - +
139U LEU* 3.4 15.5 - - + +
143U ARG* 2.6 33.7 + - - -
92V ASN* 3.4 16.9 + - - +
93V VAL* 1.3 73.2 - - - +
95V PHE* 1.3 69.8 + - + +
106V GLY 2.8 16.8 + - - +
126V TYR* 2.6 34.0 + - - +
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Residues in contact with PHE 95 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135U LYS* 3.6 39.5 - - + +
136U ALA* 3.4 40.6 - - + -
139U LEU* 3.9 13.0 - - + -
93V VAL* 3.5 3.7 - - - +
94V ASP* 1.3 88.7 - - + +
96V VAL* 1.3 67.9 + - - +
97V ASP* 3.5 18.4 - - - +
104V TYR* 3.2 34.3 - - + -
105V VAL* 3.4 5.9 - - - +
106V GLY* 3.2 37.9 + - - +
126V TYR* 4.1 0.4 - - - -
130V GLU* 5.8 0.2 - - - -
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Residues in contact with VAL 96 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93V VAL* 3.8 18.8 - - + -
95V PHE* 1.3 79.3 - - - +
97V ASP* 1.3 65.5 + - - +
98V LEU 4.3 0.3 + - - -
103V PHE* 4.2 18.8 - - + -
104V TYR 3.5 3.4 - - - -
105V VAL* 4.1 13.7 - - + -
135V LYS* 4.4 24.2 - - + -
139V LEU* 4.0 22.2 - - + -
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Residues in contact with ASP 97 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103U PHE* 5.9 0.2 - - - -
135U LYS* 2.8 36.0 + - - +
95V PHE* 3.5 16.1 - - - +
96V VAL* 1.3 79.6 - - - +
98V LEU* 1.3 59.5 + - - +
99V ASN* 3.9 18.8 - - - +
102V LYS 3.7 0.3 - - - +
103V PHE* 3.2 7.6 - - - -
104V TYR* 2.7 53.4 + - + +
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Residues in contact with LEU 98 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96V VAL 4.3 0.8 + - - -
97V ASP* 1.3 72.6 - - - +
99V ASN* 1.3 65.9 + - - +
100V ASN 3.9 18.4 - - - +
101V GLY* 4.0 13.0 - - - -
102V LYS 3.3 13.9 - - - +
103V PHE* 3.8 33.7 - - + -
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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