Contacts of the strand formed by residues 26 - 32 (chain G) 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 ASP 26 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24G GLY 3.4 10.8 - - - +
25G TRP* 1.3 77.7 - - - +
27G LEU* 1.3 62.4 + - - +
28G MET* 3.5 23.5 + - + +
40G TYR* 3.3 6.8 - - - -
41G SER 2.8 34.5 + - - +
46H TYR* 2.6 30.8 + - + -
107H LYS* 2.9 32.2 + - - +
109H GLN* 5.7 0.5 + - - -
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Residues in contact with LEU 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G PHE* 4.3 5.8 - - + -
12G GLY* 4.2 16.2 - - - +
14G LEU 4.7 4.3 - - - +
15G GLY* 5.9 2.2 - - - -
26G ASP* 1.3 73.1 - - - +
28G MET* 1.4 63.9 + - - +
29G GLN* 5.3 3.8 + - + -
38G TYR* 4.0 40.8 - - + -
39G MET 3.4 13.7 - - - +
40G TYR* 3.8 43.3 - - + +
105H SER* 5.0 7.6 - - - +
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Residues in contact with MET 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G ASP* 3.9 22.2 - - + +
27G LEU* 1.4 81.6 - - - +
29G GLN* 1.3 65.9 + - - +
30G ASN* 4.4 7.4 - - - +
38G TYR* 3.2 7.6 - - - +
39G MET* 2.6 45.7 + - + +
41G SER* 3.8 30.1 - - - +
46H TYR* 5.9 0.7 - - - -
89H ARG* 6.2 0.2 - - - +
105H SER 5.3 6.3 - - - +
107H LYS* 4.4 21.8 - - + -
109H GLN* 3.3 40.6 - - - +
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Residues in contact with GLN 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G LEU* 5.3 3.5 + - + +
28G MET* 1.3 77.0 - - - +
30G ASN* 1.3 68.8 + - - +
37G ILE 3.4 4.9 - - - -
38G TYR* 3.3 34.7 + - + -
89H ARG* 2.8 28.9 + - - +
90H TRP* 3.5 31.3 - - + -
103H LYS 2.8 22.9 + - - +
104H LEU* 3.8 11.4 - - + +
105H SER* 2.8 45.6 + - - +
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Residues in contact with ASN 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G MET* 4.4 5.1 - - - +
29G GLN* 1.3 91.6 + - - +
31G ILE* 1.3 66.4 + - - +
36G PRO* 3.5 3.1 - - - +
37G ILE* 2.7 36.2 + - + +
39G MET* 3.5 28.4 - - + +
89H ARG* 4.0 11.9 + - - +
90H TRP* 3.6 2.1 - - - -
114H PHE* 3.6 30.2 - - + +
116H LEU* 3.9 4.6 - - + +
117H GLY* 3.5 26.1 + - - -
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Residues in contact with ILE 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G ASN* 1.3 81.7 + - - +
32G MET* 1.3 62.3 + - - +
34G ASP* 3.8 15.9 - - - +
35G MET 3.2 22.0 - - - +
36G PRO* 4.1 11.7 - - + -
132G ARG* 5.7 1.2 + - - -
88H VAL* 3.7 35.9 - - + +
89H ARG* 3.7 24.5 + - - +
90H TRP* 4.0 16.2 - - + -
91H GLN* 4.9 6.7 - - + +
116H LEU* 3.7 15.6 - - - +
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Residues in contact with MET 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C CYS* 4.5 19.7 - - - -
30G ASN 4.0 0.8 + - - -
31G ILE* 1.3 74.4 - - - +
33G ASN* 1.4 94.2 + - - +
34G ASP 3.3 0.9 - - - -
35G MET* 2.8 24.8 + - - +
37G ILE* 3.9 25.3 - - + +
134G VAL* 4.2 23.3 - - + -
136G LEU* 5.0 9.4 - - + -
165G LEU* 4.7 6.1 - - - -
114H PHE* 4.0 19.7 - - - -
116H LEU* 3.7 19.5 - - + -
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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