Contacts of the strand formed by residues 88 - 92 (chain B) in PDB entry 3HEI
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 VAL 88 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 3.4 37.0 - - + +
68B ILE* 3.8 24.2 - - + -
69B LEU 3.7 4.0 - - - -
70B TYR* 3.4 25.4 - - + +
85B LYS* 3.0 36.2 + - + +
86B ASP 4.2 5.4 - - - +
87B GLN* 1.3 77.9 - - - +
89B ARG* 1.3 61.6 + - - +
90B TRP 3.8 8.5 - - - +
91B GLN* 4.3 10.3 - - + -
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Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A MET* 6.1 0.6 - - - +
29A GLN* 2.8 35.3 + - - +
30A ASN* 3.9 11.7 + - - +
31A ILE* 3.2 15.4 + - - +
69B LEU* 2.8 16.2 + - + +
70B TYR 4.1 0.4 - - - -
71B LEU* 3.9 32.5 - - + +
87B GLN 3.1 1.3 + - - +
88B VAL* 1.3 72.5 - - - +
90B TRP* 1.3 68.2 + - - +
104B LEU* 3.7 38.2 - - + +
105B SER 4.7 1.8 + - - -
106B GLU* 2.8 48.0 + - - +
128B TYR* 4.2 8.7 - - + -
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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
----------------------------------------------------------
29A GLN* 3.5 40.7 + - + -
30A ASN 3.5 25.4 - - - -
31A ILE* 3.6 10.2 - - + +
36A PRO* 3.4 26.9 - - + -
37A ILE 4.1 3.6 - - - -
38A TYR* 3.5 29.4 - + - -
51B CYS* 5.1 4.3 - - - -
69B LEU* 2.9 34.0 + - + +
88B VAL* 3.9 1.4 - - - +
89B ARG* 1.3 91.9 - - - +
91B GLN* 1.3 88.8 + - - +
102B GLU* 2.7 30.7 + - + +
103B LYS 4.3 0.6 + - - -
104B LEU* 3.9 37.2 - - + -
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Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 5.2 2.0 - - + +
34A ASP 5.7 1.2 - - - +
36A PRO* 6.2 0.2 - - - +
67B TYR 3.5 6.1 - - - +
68B ILE* 3.7 24.7 - - + +
88B VAL* 4.3 9.0 - - + -
90B TRP* 1.3 102.3 + - - +
92B CYS* 1.3 59.4 + - - +
93B ASN* 3.2 34.0 + - + +
102B GLU* 4.1 4.5 - - - +
133B ILE* 4.2 2.2 - - + +
132N PRO 5.3 0.5 - - - +
133N ILE 3.2 15.2 + - - +
134N HIS* 2.9 45.4 + - - +
135N GLN 5.4 0.2 - - - +
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Residues in contact with CYS 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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25B TRP* 5.3 3.8 - - - -
49B ILE* 5.6 0.2 - - - -
50B ILE 5.3 0.2 - - - -
51B CYS* 2.2 59.0 - - + -
52B PRO* 4.1 11.0 - - + -
65B GLU 4.6 0.5 - - - +
66B GLN* 3.2 25.8 - - - +
67B TYR* 2.7 28.1 + - - +
69B LEU* 4.1 28.2 - - - +
91B GLN* 1.3 69.0 - - - +
93B ASN* 1.4 56.5 + - - +
94B ARG 3.6 2.9 - - - -
95B PRO* 5.0 0.8 - - - +
102B GLU* 4.8 0.9 - - - -
133B ILE* 4.4 0.2 - - - +
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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
------------------------------------------------------------
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