Contacts of the strand formed by residues 81 - 94 (chain B) in PDB entry 1H1B
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 GLN 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B VAL 3.7 1.7 - - - +
67B VAL 3.7 0.3 - - - -
68B LEU* 2.8 49.1 + - + +
79B THR 3.7 3.8 + - - +
80B ARG* 1.3 77.6 - - - +
82B VAL* 1.3 62.1 + - - +
83B PHE* 3.9 11.2 - - + -
111B SER 4.5 0.2 - - - +
112B ALA* 3.3 10.3 - - - -
113B THR* 2.7 55.4 + - - -
115B ASN* 3.9 10.5 - - - +
118B VAL* 3.8 17.2 - - + +
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ARG* 4.1 28.7 - - - +
66B VAL 3.5 7.2 - - - +
67B VAL* 4.3 17.5 - - + -
80B ARG* 4.5 15.7 - - + -
81B GLN* 1.3 77.1 - - - +
83B PHE* 1.3 79.9 + - - +
1F NAG 3.8 23.0 + - - +
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Residues in contact with PHE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ARG* 3.5 8.1 + - - +
66B VAL* 2.8 40.2 + - + +
68B LEU* 3.4 34.3 - - + -
81B GLN* 3.9 20.4 - - + -
82B VAL* 1.3 82.0 - - - +
84B ALA* 1.3 59.8 + - - +
108B LEU* 4.1 22.7 - - + -
109B ASN* 3.5 17.0 - - - +
110B GLY* 3.5 33.2 - - - -
111B SER 3.4 24.7 - - - -
112B ALA* 3.8 4.0 - - - -
1F NAG 4.1 13.8 - - - -
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL* 6.1 2.9 - - + -
63B ARG 5.5 1.8 - - - +
65B VAL 4.0 7.0 - - - +
66B VAL* 4.6 3.8 - - - -
83B PHE* 1.3 73.8 - - - +
85B VAL* 1.3 64.7 + - - +
108B LEU* 3.3 7.3 - - - +
109B ASN* 2.9 38.6 + - + +
1F NAG 3.7 14.8 - - - +
2F FUC 3.9 23.1 - - + -
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PRO* 4.2 8.8 - - + +
99A VAL* 3.9 20.8 - - - +
59B VAL* 6.0 0.2 - - + -
62B VAL* 3.9 37.0 - - + -
63B ARG* 6.0 1.1 + - - -
65B VAL* 4.3 14.4 + - + -
66B VAL* 4.2 18.6 - - + -
84B ALA* 1.3 76.7 - - - +
86B GLN* 1.3 64.3 + - - +
87B ARG 4.1 4.7 - - - +
88B ILE* 4.0 21.3 - - + -
106B LEU* 4.3 24.7 - - + -
107B GLN 3.8 5.6 - - - +
108B LEU* 4.8 0.7 - - - +
109B ASN* 5.4 0.7 - - - +
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Residues in contact with GLN 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ASP* 2.9 49.1 - - - +
98A PRO* 4.2 5.6 - - - -
99A VAL* 5.4 1.1 - - - -
84B ALA 3.7 0.4 + - - -
85B VAL* 1.3 75.2 - - - +
87B ARG* 1.3 81.0 + - - +
107B GLN* 2.8 24.0 + - + +
108B LEU 3.4 19.0 + - - +
109B ASN* 3.2 34.6 + - + +
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Residues in contact with ARG 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A GLY* 3.1 31.1 + - - +
94A TYR 3.2 5.6 - - - -
95A ASP* 4.7 2.8 + - + -
100A LEU* 3.4 29.7 - - - +
101A ASN* 4.1 7.3 + - - -
85B VAL* 4.3 0.7 - - - +
86B GLN* 1.3 105.3 + - - +
88B ILE* 1.3 64.7 + - - +
89B PHE* 3.7 19.5 - - + -
105B ILE 3.8 0.5 - - - +
106B LEU* 3.4 6.2 - - - +
107B GLN* 2.9 54.1 + - + +
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLU* 3.6 26.7 - - - +
91A ASN 3.9 0.2 - - - -
92A GLY 2.8 20.8 + - - -
94A TYR* 2.8 34.1 + - + +
98A PRO* 4.0 18.4 - - + -
59B VAL* 5.2 5.4 - - + -
62B VAL* 4.0 31.2 - - + +
85B VAL* 4.0 10.8 - - + -
87B ARG* 1.3 80.0 - - - +
89B PHE* 1.3 65.9 + - - +
90B GLU* 4.2 9.4 - - + +
104B VAL* 3.6 22.9 - - + -
105B ILE 3.7 3.4 - - - -
106B LEU* 4.0 7.4 - - + -
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Residues in contact with PHE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLU 3.4 4.7 - - - +
91A ASN* 3.5 21.3 - - - -
92A GLY* 3.2 31.6 - - - -
51B PHE* 4.3 5.8 - + - -
87B ARG* 3.7 26.7 - - + -
88B ILE* 1.3 77.9 - - - +
90B GLU* 1.3 67.6 + - - +
104B VAL* 3.4 2.6 - - - +
105B ILE* 3.2 40.4 + - + +
107B GLN* 4.2 12.6 - - - -
237B TRP* 3.6 9.1 - + + -
241B ILE* 3.7 52.5 - - + -
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Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ILE* 3.7 29.6 - - - +
89A PHE* 3.4 3.6 - - - +
90A GLU* 3.0 42.7 + - + +
237A TRP* 5.2 1.4 + - - -
56B ALA* 4.2 14.9 - - - +
59B VAL* 4.0 15.4 - - - +
60B ALA* 6.0 0.7 - - - -
88B ILE* 4.2 9.4 - - + +
89B PHE* 1.3 79.1 - - - +
91B ASN* 1.3 62.3 + - - +
92B GLY 3.9 1.1 - - - -
94B TYR* 4.2 14.3 - - + -
103B ILE 4.1 7.0 - - - +
104B VAL* 3.7 25.7 - - + +
237B TRP* 3.8 7.4 + - - -
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Residues in contact with ASN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE* 3.3 20.1 - - - -
241A ILE* 5.6 0.5 - - - +
90B GLU* 1.3 74.8 - - - +
92B GLY* 1.3 61.8 + - - +
94B TYR* 3.6 2.0 + - - +
101B ASN* 3.8 16.4 + - - +
103B ILE* 4.7 5.4 + - + +
234B PHE* 4.4 15.8 - - + -
237B TRP* 3.7 53.1 - - + +
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Residues in contact with GLY 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ARG* 3.2 18.1 + - - +
88A ILE 2.7 20.8 + - - -
89A PHE* 3.3 27.9 - - - -
91B ASN* 1.3 74.0 - - - +
94B TYR* 1.3 63.8 + - - -
95B ASP* 3.3 2.3 + - - +
100B LEU* 4.1 0.7 - - - +
101B ASN* 3.2 20.1 - - - +
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Residues in contact with TYR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ARG* 3.1 2.8 - - - -
88A ILE* 2.6 55.4 + - + +
56B ALA* 3.6 29.6 - - + -
57B HIS* 3.2 36.3 - - - -
60B ALA* 4.5 13.2 - - + +
90B GLU* 4.2 16.2 - - + +
91B ASN 3.6 2.2 - - - +
92B GLY* 1.3 74.3 - - - +
95B ASP* 1.3 75.1 + - - +
98B PRO* 3.6 24.9 - - + +
99B LEU* 3.7 11.6 - + + -
100B LEU 3.6 4.3 - - - -
101B ASN* 3.4 22.3 + - - +
102B ASP* 3.8 17.9 - - - -
103B ILE 5.2 0.4 - - - +
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Residues in contact with ASP 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLN* 2.8 35.6 - - - +
87A ARG* 4.4 3.2 + - + +
92B GLY 3.3 2.9 + - - +
94B TYR* 1.3 76.6 - - - +
98B PRO* 1.3 60.4 - - - +
99B LEU* 2.8 91.4 + - - +
100B LEU* 3.1 25.8 + - + +
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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