Contacts of the strand formed by residues 83 - 91 (chain B) in PDB entry 4YHP
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 ALA 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B GLN* 3.7 23.6 - - + -
37B GLN 3.3 21.3 - - - +
38B ARG* 4.0 6.7 - - + +
39B PRO* 4.9 4.0 - - - -
81B ASP 3.1 8.8 + - - +
82B GLU* 1.3 76.6 - - - +
84B ASP* 1.3 65.4 + - - +
85B TYR* 3.7 7.5 - - + -
103B THR 3.6 0.9 - - - +
104B LYS* 3.4 5.6 - - - +
105B VAL 2.8 29.9 + - - -
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Residues in contact with ASP 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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35B TYR 3.8 0.5 - - - +
36B GLN* 3.7 1.4 - - - -
37B GLN* 2.7 52.6 + - + +
83B ALA* 1.3 72.2 - - - +
85B TYR* 1.3 60.6 + - - +
86B TYR* 3.9 29.6 + - + +
102B GLY* 5.6 0.4 - - - -
103B THR 3.3 6.3 - - - +
104B LYS* 3.2 44.0 + - - +
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Residues in contact with TYR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B GLN* 2.8 26.5 + - - -
20B ILE* 3.9 18.6 - - + -
34B TRP* 5.0 2.2 - - + -
35B TYR 3.2 16.2 - - - +
36B GLN* 3.0 39.4 + - + -
46B VAL* 4.9 1.6 - - + -
61B PHE* 3.9 10.6 - + - -
72B LEU* 3.6 20.2 - - + -
74B ILE* 3.5 22.3 - - + +
81B ASP* 2.7 32.4 + - - +
83B ALA* 3.7 12.3 - - + -
84B ASP* 1.3 75.1 - - - +
86B TYR* 1.3 57.8 + - - +
102B GLY* 3.3 1.0 - - - -
103B THR 2.8 23.8 + - - +
105B VAL* 3.6 31.4 - - + -
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Residues in contact with TYR 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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39A GLN* 3.3 18.9 + - - -
43A LYS 3.7 3.6 + - - -
44A GLY* 3.5 11.8 - - - -
45A LEU* 3.7 44.2 - - + -
6B GLN* 3.4 3.6 - - - -
34B TRP* 3.3 6.9 - - - -
35B TYR* 2.9 44.0 + - + -
37B GLN* 3.3 26.0 + - + -
84B ASP* 3.9 30.6 + - + -
85B TYR* 1.3 74.8 - - - +
87B CYS* 1.3 65.4 + - - +
99B PHE* 4.4 6.7 - - + -
100B GLY 3.6 13.9 - - - -
101B THR 3.7 9.7 + - - -
102B GLY* 3.5 25.4 - - - -
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Residues in contact with CYS 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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4B LEU* 4.0 3.1 - - - -
6B GLN* 3.0 25.0 + - - -
22B CYS* 2.0 48.5 - - + -
32B VAL* 4.0 3.1 - - + -
33B HIS 3.2 7.0 - - - +
34B TRP* 3.5 23.3 - - + -
86B TYR* 1.3 73.7 - - - +
88B GLN* 1.3 61.4 + - - +
99B PHE* 3.3 5.5 - - - -
100B GLY* 2.8 37.3 + - - -
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Residues in contact with GLN 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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106A TRP 3.0 21.8 + - - -
107A HIS* 3.4 4.0 - - - +
108A PHE* 4.8 0.4 - - - -
4B LEU* 4.5 0.7 - - - -
32B VAL* 3.5 1.3 - - - +
33B HIS* 2.8 53.1 + - - +
35B TYR* 2.6 42.2 + - + -
87B CYS* 1.3 78.9 - - - +
89B VAL* 1.3 87.4 + - - +
97B TYR* 3.3 26.2 - - + -
98B VAL 3.2 13.7 - - - +
99B PHE* 3.9 20.9 - - + -
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Residues in contact with VAL 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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2B TYR* 4.9 7.9 - - + -
4B LEU* 4.1 13.7 - - + -
27B ILE* 3.6 28.5 - - + -
30B ILE* 3.9 19.1 - - + -
31B SER 3.6 19.1 - - - +
32B VAL* 4.1 6.3 - - + -
33B HIS* 4.6 0.9 - - - -
88B GLN* 1.3 91.7 + - - +
90B TRP* 1.3 63.8 + - - +
91B ASP* 4.8 1.6 - - + +
97B TYR* 3.7 0.5 - - - -
98B VAL* 2.9 55.0 + - + +
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Residues in contact with TRP 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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33A TRP* 6.6 0.2 - + - -
50A ASP* 4.9 5.2 + - - -
59A TYR* 6.2 0.7 - + - -
99A GLU* 5.1 1.2 + - - -
106A TRP* 3.9 52.2 + + + +
30B ILE* 5.7 4.6 - - - +
31B SER 4.9 2.0 + - - -
33B HIS* 5.0 1.6 + - - -
88B GLN* 3.7 1.0 - - - +
89B VAL* 1.3 77.4 - - - +
91B ASP* 1.3 61.5 + - - +
92B ASP* 3.4 40.1 + - + +
95B ASN* 3.9 30.0 + - + -
96B ALA 3.7 19.5 - - - +
97B TYR* 3.5 44.8 - + + -
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Residues in contact with ASP 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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2B TYR* 3.9 29.1 + - + +
30B ILE* 6.6 0.2 - - - -
89B VAL* 4.1 3.2 - - + +
90B TRP* 1.3 70.6 - - - +
92B ASP* 1.3 56.9 + - - +
93B SER* 3.1 23.1 + - - -
94B ILE* 3.3 33.1 - - + +
95B ASN* 2.8 31.5 + - - -
96B ALA 2.9 23.2 + - - +
98B VAL* 4.9 7.4 - - + -
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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