Contacts of the strand formed by residues 61 - 66 (chain B) in PDB entry 3HS3
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 MET 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A MET* 4.0 26.5 - - + +
93A LEU* 3.9 25.8 - - + -
115A ASN* 4.4 18.4 - - - +
59B SER* 3.1 32.0 + - - +
60B LYS* 1.3 82.5 - - - +
62B ILE* 1.3 65.6 + - - +
63B GLY 4.2 0.2 - - - -
91B THR* 3.3 14.4 - - - +
93B LEU* 4.5 12.3 - - + -
115B ASN* 3.8 16.8 - - + +
117B VAL* 3.6 11.0 - - + -
118B ASP* 2.9 26.7 + - - +
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Residues in contact with ILE 62 (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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61B MET* 1.3 81.6 - - - +
63B GLY* 1.3 72.8 + - - +
64B ILE* 3.6 11.1 + - + +
85B ILE* 4.0 31.2 - - + -
90B TYR* 3.8 24.5 - - + -
91B THR 3.0 6.7 + - - -
92B ALA* 3.5 3.8 - - - -
93B LEU* 2.8 24.4 + - - -
119B GLY 3.5 22.2 - - - +
121B ILE* 4.3 8.7 - - + -
293B LEU* 3.7 28.9 - - + -
294B LEU* 5.8 1.3 - - + -
297B MET* 3.9 14.1 - - + -
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Residues in contact with GLY 63 (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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62B ILE* 1.3 74.3 - - - +
64B ILE* 1.3 60.6 + - - +
93B LEU 3.2 9.2 - - - -
112B PHE* 3.7 29.8 - - - -
117B VAL* 3.9 9.2 - - - +
119B GLY 2.9 12.7 + - - -
120B ILE* 3.2 1.8 - - - -
121B ILE 2.8 26.3 + - - -
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Residues in contact with ILE 64 (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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62B ILE* 3.9 11.9 - - + +
63B GLY* 1.3 79.1 - - - +
65B ILE* 1.3 68.0 + - - +
66B ILE* 3.9 9.4 - - + -
78B ILE* 3.6 31.2 - - + -
81B ILE* 3.7 37.0 - - + -
82B GLN* 5.7 0.9 - - + +
85B ILE* 4.8 2.7 - - + -
92B ALA* 3.7 28.3 - - + -
93B LEU 2.9 7.1 + - - -
94B ILE* 3.3 16.1 - - + +
95B SER 2.9 26.2 + - - +
112B PHE* 3.5 2.2 - - - -
121B ILE* 3.1 15.5 - - + +
140B TYR* 5.0 0.7 - - + -
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Residues in contact with ILE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 1.3 72.2 - - - +
66B ILE* 1.3 60.8 + - - +
95B SER* 3.4 11.4 - - - +
97B SER* 4.3 14.4 - - - +
105B TYR* 3.6 33.7 - - + +
108B ALA* 3.8 26.9 - - + -
109B ILE* 4.2 15.3 - - + -
112B PHE* 3.5 25.1 - - + -
120B ILE* 5.1 0.7 - - + -
121B ILE 3.0 6.4 + - - +
122B THR* 3.6 26.5 - - - +
123B SER* 3.6 10.3 + - - +
140B TYR* 2.7 26.3 + - - -
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Residues in contact with ILE 66 (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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64B ILE* 3.9 4.9 - - + -
65B ILE* 1.3 75.3 - - - +
67B PRO* 1.3 72.2 - - + +
68B ASP 3.9 8.1 - - - +
69B LEU* 3.4 28.9 - - + -
74B TYR* 4.7 6.5 - - + +
77B ILE* 5.5 0.9 - - + -
78B ILE* 3.5 30.7 - - + -
94B ILE* 3.9 12.1 - - + -
95B SER 3.3 2.0 + - - -
96B PHE* 3.1 39.9 - - + -
97B SER* 3.0 24.6 + - - -
123B SER* 4.9 1.3 - - - -
140B TYR* 2.9 22.7 - - + +
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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