Contacts of the helix formed by residues 988 - 996 (chain A) in PDB entry 4EZJ
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 THR 988 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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888A ILE* 5.8 0.7 - - - +
949A ASN* 5.7 0.7 + - - -
986A VAL* 3.5 21.2 - - + +
987A LEU* 1.3 78.7 - - - +
989A PRO* 1.4 74.1 - - + +
990A ASP* 2.7 22.2 + - - -
991A PHE* 3.0 21.8 + - - -
992A LEU* 3.1 13.6 + - - +
1079A GLY 3.4 20.9 - - - +
1080A TRP* 4.0 7.5 - - + -
1083A GLN* 3.8 28.7 - - + -
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Residues in contact with PRO 989 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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904A ASP* 3.4 30.9 - - - +
988A THR* 1.4 87.5 - - - +
990A ASP* 1.4 54.1 + - - +
992A LEU* 3.8 13.1 - - + +
993A PHE* 2.9 29.5 + - - +
997A THR 4.8 1.2 - - - +
1079A GLY* 3.7 24.9 - - - -
1080A TRP* 3.5 35.0 - - + +
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Residues in contact with ASP 990 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888A ILE* 3.6 18.4 - - - +
892A GLN* 3.2 20.9 + - - +
903A LYS 4.2 4.3 - - - +
904A ASP 3.4 18.2 - - - +
907A LEU* 3.9 17.3 - - + +
908A ASN 5.0 0.2 + - - -
988A THR* 2.7 30.7 + - - -
989A PRO* 1.4 74.1 - - - +
991A PHE* 1.3 73.8 + - - +
993A PHE* 3.7 3.3 + - - +
994A VAL* 3.2 26.5 + - - +
1080A TRP* 3.3 22.7 - - + -
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Residues in contact with PHE 991 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888A ILE* 3.9 24.2 - - + -
907A LEU* 3.5 20.2 - - + -
928A PHE* 3.4 31.4 - + + -
932A CYS* 4.0 9.2 - - - -
949A ASN* 6.1 0.4 - - + -
952A ILE* 4.4 6.3 - - + -
960A LEU* 3.9 26.7 - - + -
986A VAL* 3.3 45.3 - - + -
987A LEU* 3.9 12.3 - - + -
988A THR* 3.0 21.6 + - - +
990A ASP* 1.3 91.5 + - - +
992A LEU* 1.4 59.2 + - - +
994A VAL* 3.0 21.1 + - - +
995A MET* 3.3 11.9 + - - +
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Residues in contact with LEU 992 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987A LEU* 3.6 35.4 - - + +
988A THR 3.1 21.7 + - - +
989A PRO* 3.9 10.3 - - + +
991A PHE* 1.4 73.7 - - - +
993A PHE* 1.4 56.9 + - - +
995A MET* 3.0 17.4 + - - +
996A GLY 3.1 0.5 + - - -
997A THR* 3.0 42.7 + - + +
998A SER* 5.7 1.6 - - - -
999A GLY 6.3 0.9 - - - +
1006A PHE* 3.6 37.7 - - + -
1075A CYS 5.0 0.7 - - - +
1076A ARG* 4.2 26.9 - - + -
1079A GLY* 6.5 0.2 - - - -
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Residues in contact with PHE 993 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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904A ASP* 3.4 25.4 - - + +
905A GLU* 3.5 50.9 - - + -
908A ASN* 3.9 25.5 + - + -
909A HIS* 5.4 2.5 - + - -
989A PRO 2.9 19.0 + - - +
990A ASP 3.8 3.4 - - - +
991A PHE 3.2 0.4 - - - -
992A LEU* 1.4 76.4 - - - +
994A VAL* 1.4 60.0 + - - +
996A GLY* 3.3 11.9 + - - -
997A THR 3.4 15.0 + - - +
998A SER* 4.8 11.7 - - - -
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Residues in contact with VAL 994 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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907A LEU* 4.0 16.4 - - + -
908A ASN* 3.5 41.2 + - - +
911A LEU* 3.9 19.7 - - + -
925A VAL* 4.0 30.8 - - + +
928A PHE* 3.9 23.6 - - + -
929A VAL* 5.8 0.2 - - - -
990A ASP 3.2 18.4 - - - +
991A PHE 3.0 7.9 + - - +
993A PHE* 1.4 75.6 - - - +
995A MET* 1.3 61.3 + - - +
996A GLY* 3.4 0.9 + - - -
1005A HIS* 4.9 1.6 - - - -
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Residues in contact with MET 995 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928A PHE* 3.6 30.3 - - + -
929A VAL* 3.9 22.7 - - + -
932A CYS* 3.8 15.9 - - + -
987A LEU* 4.0 10.1 - - + -
991A PHE 3.3 9.1 + - - +
992A LEU* 3.0 17.6 + - - +
994A VAL* 1.3 77.2 - - - +
996A GLY* 1.3 55.7 + - - +
997A THR* 4.5 0.2 - - + -
1003A SER* 2.9 15.5 + - - -
1004A PRO* 5.3 0.3 - - - +
1005A HIS* 3.2 32.2 + - - +
1006A PHE* 4.0 21.3 - - + +
1009A PHE* 3.7 41.5 - - + -
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Residues in contact with GLY 996 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992A LEU 3.1 1.4 + - - -
993A PHE* 3.3 9.8 + - - -
994A VAL 3.2 4.6 - - - -
995A MET* 1.3 77.7 - - - +
997A THR* 1.3 58.2 + - - +
1001A LYS* 4.1 3.8 - - - +
1003A SER* 3.3 18.6 - - - -
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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