Contacts of the strand formed by residues 90 - 98 (chain B) in PDB entry 2HP4
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 GLY 90 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37B PHE* 3.6 6.5 - - - -
38B GLN 3.5 9.6 - - - -
39B PRO 4.2 0.2 - - - -
40B ARG 3.9 6.1 - - - -
88B ASN 3.5 1.8 + - - -
89B GLU* 1.3 75.3 - - - +
91B TYR* 1.3 65.5 + - - -
92B TYR* 4.2 1.6 - - - -
108B VAL 3.8 0.2 - - - +
109B PRO 3.7 0.3 - - - -
110B VAL* 2.8 35.6 + - - +
111B PHE* 3.5 17.1 - - - -
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Residues in contact with TYR 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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42A ALA* 5.1 6.7 - - + +
43A ALA* 4.7 20.5 + - + +
37B PHE* 3.3 6.3 - - - -
38B GLN* 2.8 43.4 + - + +
39B PRO 3.9 5.4 - - - -
40B ARG* 3.8 31.6 + - - -
90B GLY* 1.3 73.7 - - - -
92B TYR* 1.3 62.0 - - - +
93B PHE* 3.9 2.9 - - - -
107B PHE* 3.5 57.0 - + + -
108B VAL 3.7 1.6 - - - -
109B PRO* 3.9 18.4 - - + -
111B PHE* 3.8 27.7 - + - -
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Residues in contact with TYR 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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18B VAL* 5.7 2.5 - - + -
20B LEU* 3.3 22.9 - - + -
35B TRP* 4.1 5.6 - - + -
36B LEU 3.3 6.5 - - - +
37B PHE* 3.3 22.7 - + - -
49B LEU* 3.8 21.8 - - + -
68B PHE* 4.7 4.9 - + - -
79B LEU* 3.7 22.7 - - + -
81B LEU* 4.2 9.3 - - + +
84B PHE* 5.1 0.2 - - - -
88B ASN* 2.6 35.9 + - - +
90B GLY 3.9 2.5 - - - -
91B TYR* 1.3 76.5 - - - +
93B PHE* 1.3 63.4 + - - +
107B PHE* 3.7 0.2 - - - -
108B VAL* 2.7 42.9 + - - +
110B VAL* 3.5 31.9 - - + -
404B GOL 2.8 19.1 + - - -
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Residues in contact with PHE 93 (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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45A SER* 4.5 2.9 - - - -
46A PRO* 3.5 34.5 - - + -
35B TRP* 3.4 12.8 - - - -
36B LEU* 2.7 82.2 + - + +
37B PHE 4.2 0.4 - - - -
38B GLN* 4.0 19.3 - - + -
46B PRO* 4.0 19.1 - - + -
91B TYR 3.9 2.7 - - - -
92B TYR* 1.3 77.6 - - - +
94B CYS* 1.3 60.4 + - - +
104B PHE* 3.9 10.3 - + - -
105B SER* 3.5 16.8 - - - +
106B HIS 3.8 9.0 - - - +
107B PHE* 3.4 29.6 - + + -
108B VAL* 5.4 0.9 - - - -
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Residues in contact with CYS 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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3B PHE* 4.2 10.7 - - + -
22B CYS* 2.0 53.4 - - + -
33B ALA* 4.5 5.2 - - + -
34B SER 3.1 10.1 - - - +
35B TRP* 3.2 30.9 - - - -
36B LEU* 4.9 0.4 - - - -
93B PHE* 1.3 77.3 - - - +
95B SER* 1.3 61.6 + - - +
104B PHE* 3.4 4.5 - - - +
105B SER* 2.9 35.3 + - - +
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Residues in contact with SER 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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102A MET* 3.6 25.3 - - - +
3B PHE* 4.0 3.1 - - - -
32B GLY 4.1 0.2 - - - +
33B ALA* 3.4 4.7 - - - +
34B SER* 3.0 32.4 + - - -
36B LEU* 3.7 8.1 - - - +
94B CYS* 1.3 75.2 - - - +
96B ALA* 1.3 62.9 + - - +
102B MET* 4.5 8.2 - - - +
103B TYR 3.0 14.1 - - - -
104B PHE* 3.6 24.2 - - - -
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Residues in contact with ALA 96 (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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3B PHE* 3.7 21.0 - - + -
24B VAL* 4.8 7.9 - - + -
26B LEU* 3.9 16.2 - - + -
29B PRO* 5.6 0.7 - - + -
31B SER* 4.1 4.5 - - - +
32B GLY 3.9 15.5 - - - +
33B ALA* 4.7 2.7 - - - -
95B SER* 1.3 76.9 - - - +
97B LEU* 1.3 66.2 + - - +
102B MET* 3.6 3.3 - - - +
103B TYR* 2.9 33.6 + - - -
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Residues in contact with LEU 97 (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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97A LEU* 4.2 23.8 - - + -
102A MET* 6.5 0.4 - - + -
26B LEU* 4.0 4.0 - - - +
29B PRO* 3.6 6.6 - - - +
30B THR* 3.0 26.8 + - - +
31B SER* 3.0 29.6 + - - +
96B ALA* 1.3 75.5 - - - +
98B SER* 1.3 63.8 + - - +
99B ASN 5.1 0.4 - - - +
100B SER* 4.5 14.6 - - - +
101B ILE 3.5 5.6 - - - +
102B MET* 3.8 44.6 - - + +
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Residues in contact with SER 98 (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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26B LEU* 4.4 7.0 - - - +
28B ASN* 2.6 34.0 + - - +
30B THR* 3.4 4.3 - - - -
97B LEU* 1.3 78.2 - - - +
99B ASN* 1.3 74.3 + - - +
100B SER 3.4 0.2 - - - -
101B ILE* 3.0 22.8 + - - +
103B TYR* 3.7 23.5 + - - -
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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