Contacts of the helix formed by residues 89 - 95 (chain 2) in PDB entry 3EXG
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 89 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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592 GLU* 3.8 13.7 - - + +
602 MET* 4.2 7.4 - - - +
632 ALA* 3.5 27.1 - - + -
802 PHE* 3.8 21.5 - - + -
862 SER 3.2 5.9 + - - +
872 MET 2.9 0.8 - - - -
882 GLN* 1.3 81.7 - - - +
902 ILE* 1.3 65.0 + - - +
912 ASP 3.0 3.4 - - - -
922 GLN* 2.9 17.7 + - - +
932 VAL* 3.4 10.4 + - - +
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Residues in contact with ILE 90 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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862 SER 3.1 12.9 + - - +
872 MET* 3.3 16.0 + - + +
882 GLN 3.6 0.2 - - - -
892 ALA* 1.3 77.9 - - - +
912 ASP* 1.3 65.5 + - - +
932 VAL* 3.2 6.5 + - + -
942 ILE* 3.0 32.8 + - + +
1322 PHE* 5.7 0.4 - - + -
1352 TRP* 4.0 18.8 - - + -
1362 TYR* 3.6 36.1 - - + +
87Z MET* 3.8 28.0 - - + +
90Z ILE* 4.5 9.0 - - + -
135Z TRP* 3.4 28.7 - - + -
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Residues in contact with ASP 91 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1371 ILE* 3.5 30.0 - - - +
1401 ALA* 4.0 12.9 - - - +
602 MET* 3.9 17.1 - - + +
882 GLN 5.1 0.2 + - - -
892 ALA 3.0 0.8 + - - -
902 ILE* 1.3 84.9 - - - +
922 GLN* 1.3 60.1 + - - +
952 ASN* 2.9 52.1 + - - +
962 SER 3.7 0.7 + - - -
84Z ASN 5.4 0.5 - - - +
87Z MET* 4.1 26.1 + - + +
88Z GLN* 4.0 18.3 - - + +
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Residues in contact with GLN 92 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1401 ALA* 3.1 28.9 + - - +
1431 PRO* 3.9 4.2 - - - +
1441 LEU* 4.1 2.3 - - - +
1741 GLN* 3.1 22.8 + - - -
602 MET* 3.8 19.3 - - - +
632 ALA* 4.2 7.9 - - + -
642 GLY* 3.6 39.6 - - - +
672 VAL* 4.1 7.0 - - + +
892 ALA 2.9 9.7 + - - +
912 ASP* 1.3 80.2 - - - +
932 VAL* 1.3 59.5 + - - +
962 SER* 2.5 41.0 + - - -
972 ALA* 3.3 21.5 + - - +
1142 PHE* 6.2 0.2 - - + -
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Residues in contact with VAL 93 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632 ALA* 5.5 0.4 - - + -
802 PHE* 4.8 9.0 - - + -
832 PHE* 6.6 0.2 - - + -
862 SER 5.7 0.2 - - - +
892 ALA* 3.4 13.0 + - + +
902 ILE* 3.2 11.7 + - - +
922 GLN* 1.3 76.3 - - + +
942 ILE* 1.3 62.2 + - + +
972 ALA* 3.1 8.2 - - - +
982 ALA* 2.9 27.7 + - - +
1142 PHE* 3.6 47.8 - - + -
1362 TYR* 4.1 25.8 - - + +
1422 LEU* 3.9 18.7 - - + +
1682 VAL* 4.5 2.5 - - + -
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Residues in contact with ILE 94 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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902 ILE* 3.0 30.6 + - + +
932 VAL* 1.3 84.3 - - + +
952 ASN* 1.3 73.3 + - - +
982 ALA* 3.3 18.5 - - + +
992 LYS* 3.4 18.9 + - - +
1362 TYR* 4.5 6.1 - - + -
1392 CYS* 3.6 31.2 - - + -
1422 LEU* 3.7 25.8 - - + -
87Z MET* 4.1 10.1 - - - -
130Z GLN* 3.8 19.1 - - - +
135Z TRP* 4.3 9.6 - - + -
266Z TRP* 5.2 0.2 - - + -
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Residues in contact with ASN 95 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1371 ILE* 3.4 22.4 - - + +
912 ASP* 2.9 29.1 + - - +
942 ILE* 1.3 73.2 - - - +
962 SER* 1.3 66.5 + - - +
972 ALA 3.6 0.3 + - - -
992 LYS* 3.1 42.5 + - - +
1002 THR* 4.1 0.5 + - - -
1032 MET* 4.1 6.4 - - - +
84Z ASN* 4.4 1.4 + - - +
87Z MET* 2.8 33.6 - - - +
127Z GLN* 3.2 40.2 + - - +
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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
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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