Contacts of the strand formed by residues 84 - 98 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26J PHE* 3.9 5.8 - - - -
72J ILE* 4.2 12.3 - - + -
75J ALA* 3.5 33.7 - - + -
76J ASN* 2.8 26.1 + - - +
79J PHE* 3.9 11.9 - + + -
80J GLY 3.5 15.9 - - - -
81J TYR 4.2 6.1 + - - +
82J ASN 3.6 0.2 - - - -
83J GLY* 1.3 79.4 + - - +
85J ALA* 1.3 81.0 + - - +
86J HIS* 3.8 16.4 - + - -
113J VAL* 4.1 11.0 - - + -
114J GLN 3.1 10.5 - - - +
115J LEU* 3.9 13.5 - - + -
151J LEU* 3.9 27.4 - - + -
155J LEU* 4.2 7.4 - - + -
119K SER* 4.5 4.0 - - - -
121K HIS* 3.3 40.0 + + - -
157K SER* 3.8 19.5 - - - -
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Residues in contact with ALA 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J PHE* 3.7 11.7 - - + -
84J TRP* 1.3 82.1 - - - +
86J HIS* 1.3 60.1 + - - +
113J VAL* 3.0 8.0 - - - +
114J GLN 2.7 29.0 + - - +
120K TYR* 2.8 57.4 - - + +
121K HIS* 3.8 4.9 - - - -
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Residues in contact with HIS 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84J TRP* 3.8 4.7 - + + -
85J ALA* 1.3 79.1 - - - +
87J SER* 1.3 62.2 + - - +
88J ILE* 5.5 0.4 - - + -
111J VAL* 4.0 15.3 - - + -
112J ARG 3.1 11.9 - - - +
113J VAL* 4.0 3.6 - - + -
147J VAL* 5.1 5.8 - - + +
151J LEU* 3.7 43.9 - - + +
120K TYR* 3.1 13.8 + - - -
121K HIS* 2.9 45.7 - + + -
122K GLU 3.1 46.4 + - - -
123K ASP* 4.9 5.6 + - - -
157K SER* 3.5 18.6 - - - -
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Residues in contact with SER 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86J HIS* 1.3 76.7 - - - +
88J ILE* 1.3 64.5 + - - +
89J THR* 3.6 6.6 + - - +
111J VAL* 3.4 7.2 - - - +
112J ARG* 2.9 42.8 + - - +
112K ARG* 5.1 6.7 - - - -
120K TYR* 3.9 18.3 + - - -
122K GLU* 3.5 17.7 - - - -
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Residues in contact with ILE 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86J HIS* 5.5 0.7 - - + -
87J SER* 1.3 73.0 - - - +
89J THR* 1.3 63.7 + - - +
90J GLN* 3.6 28.9 - - - +
91J GLN* 4.2 4.5 - - + +
109J ALA* 5.1 3.1 - - + -
110J PHE 3.5 7.2 - - - +
111J VAL* 4.7 6.5 - - + -
147J VAL* 3.9 25.1 - - + -
110K PHE* 3.8 31.6 - - + -
122K GLU* 2.9 32.5 + - + +
123K ASP* 3.7 33.4 - - - +
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Residues in contact with THR 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87J SER* 3.6 6.6 + - - +
88J ILE* 1.3 73.9 - - - +
90J GLN* 1.3 64.9 + - - +
110J PHE* 2.8 22.7 + - - +
112J ARG* 3.9 28.0 - - + -
122J GLU* 2.7 30.5 + - - +
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Residues in contact with GLN 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88J ILE* 3.1 10.3 - - - +
89J THR* 1.3 86.5 + - - +
91J GLN* 1.3 66.4 + - - +
92J ASN* 3.7 33.1 - - - +
109J ALA* 3.4 1.4 - - - -
110J PHE* 2.8 49.5 + - + -
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Residues in contact with GLN 91 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88J ILE* 4.2 4.0 - - + +
90J GLN* 1.3 80.7 + - - +
92J ASN* 1.3 65.6 + - - +
93J VAL 4.3 0.2 + - - -
107J VAL* 3.7 18.8 - - + +
108J CYS 3.3 11.7 - - - +
109J ALA* 3.9 2.1 - - - +
143J ARG* 2.9 69.4 + - - +
146J ALA* 3.8 5.9 - - - +
147J VAL* 3.5 16.0 - - - +
110K PHE* 3.3 35.7 - - + -
124K VAL* 3.8 1.4 - - - +
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Residues in contact with ASN 92 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I ARG* 4.8 4.1 + - - +
90J GLN* 3.7 23.1 - - - +
91J GLN* 1.3 76.0 + - - +
93J VAL* 1.3 76.8 + - - +
94J ASP* 3.4 13.4 + - - +
107J VAL* 3.6 2.4 - - - -
108J CYS* 2.9 50.4 + - - -
110J PHE* 5.6 0.4 - - + -
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Residues in contact with VAL 93 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92J ASN* 1.3 80.4 + - - +
94J ASP* 1.3 62.6 + - - +
95J PHE* 3.8 13.5 - - - +
96J VAL* 3.9 25.1 - - + -
106J GLY 3.9 2.7 - - - -
107J VAL* 3.8 20.4 - - + -
139J LEU* 4.5 7.0 - - + -
143J ARG* 3.5 39.0 - - - +
94K ASP* 5.3 0.7 - - - +
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Residues in contact with ASP 94 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93I VAL* 5.8 0.2 - - - -
139I LEU* 3.5 14.6 - - + +
143I ARG* 2.6 33.8 + - - -
92J ASN* 3.4 19.0 + - - +
93J VAL* 1.3 73.3 - - - +
95J PHE* 1.3 72.3 + - + +
106J GLY 2.7 17.6 + - - +
108J CYS* 4.8 0.2 - - - -
126J TYR* 2.6 32.9 + - - +
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Residues in contact with PHE 95 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135I LYS* 3.6 42.0 - - + +
136I ALA* 3.5 37.7 - - + -
139I LEU* 4.1 7.0 - - + -
93J VAL* 3.4 3.5 - - - +
94J ASP* 1.3 90.2 - - + +
96J VAL* 1.3 70.0 + - - +
97J ASP* 3.7 17.5 - - - +
104J TYR* 3.1 36.3 - - + -
105J VAL* 3.4 4.6 - - - +
106J GLY* 3.3 36.0 + - - +
126J TYR* 4.0 5.4 - - - -
130J GLU* 5.8 0.4 - - - -
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Residues in contact with VAL 96 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93J VAL* 3.9 17.7 - - + -
95J PHE* 1.3 80.4 - - - +
97J ASP* 1.3 64.9 + - - +
98J LEU 4.2 0.5 + - - -
103J PHE* 4.2 21.1 - - + -
104J TYR 3.6 3.6 - - - -
105J VAL* 4.2 11.0 - - + -
135J LYS* 4.4 24.7 - - + -
139J LEU* 4.0 22.9 - - + -
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Residues in contact with ASP 97 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135I LYS* 3.0 33.1 + - - +
95J PHE* 3.7 13.5 - - - +
96J VAL* 1.3 82.0 + - - +
98J LEU* 1.3 59.9 + - - +
99J ASN* 3.9 19.5 - - - +
103J PHE* 3.2 7.1 - - - -
104J TYR* 2.7 51.7 + - + +
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Residues in contact with LEU 98 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96J VAL 4.2 0.8 + - - -
97J ASP* 1.3 71.6 - - - +
99J ASN* 1.3 67.5 + - - +
100J ASN 3.8 22.0 - - - +
101J GLY* 4.0 12.1 - - - -
102J LYS 3.4 11.4 - - - +
103J PHE* 3.8 34.5 - - + -
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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