Contacts of the strand formed by residues 989 - 995 (chain A) in PDB entry 4Z96
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 LEU 989 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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940A ARG* 4.8 2.7 - - - +
979A GLN* 3.3 46.4 - - + +
988A MET* 1.3 83.8 - - + +
990A VAL* 1.3 63.6 + - - +
991A THR* 4.3 0.3 + - - +
1008A LEU* 4.6 19.0 - - + +
1009A LEU 3.3 12.6 - - - +
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Residues in contact with VAL 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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988A MET* 3.5 31.6 + - + -
989A LEU* 1.3 75.4 - - - +
991A THR* 1.3 68.8 + - - +
992A VAL* 4.8 2.5 - - + -
1008A LEU* 3.2 5.0 - - - -
1009A LEU* 2.5 57.8 + - + +
1011A ILE* 3.8 19.3 - - + -
1063A PHE* 3.9 31.6 - - + -
1075A PRO 5.4 3.4 - - - +
1077A LEU* 5.4 4.9 - - + -
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Residues in contact with THR 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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949A ILE* 3.9 35.9 - - + +
989A LEU 5.8 0.2 - - - +
990A VAL* 1.3 74.5 - - - +
992A VAL* 1.3 61.6 + - - +
1007A PHE 3.6 4.7 - - - -
1008A LEU* 3.6 20.2 - - + -
1074A ARG* 5.4 2.6 + - + +
1075A PRO 3.6 9.6 + - - -
1076A TRP* 3.4 20.7 - - - +
1077A LEU* 3.1 23.0 + - - +
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Residues in contact with VAL 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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949A ILE 5.4 0.3 + - - -
990A VAL* 3.8 1.3 - - + +
991A THR* 1.3 79.0 - - - +
993A ALA* 1.3 66.3 + - - +
1006A PRO* 3.2 10.9 - - - +
1007A PHE* 2.7 78.1 + - + +
1009A LEU* 3.7 28.3 - - + -
1024A ILE* 5.1 1.1 - - + -
1076A TRP* 5.1 0.4 - - - -
1077A LEU* 3.3 21.1 - - + +
1079A LEU* 3.7 26.2 - - + -
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Residues in contact with ALA 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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947A TYR 3.8 19.5 - - - +
948A LYS* 4.0 13.7 - - + -
992A VAL* 1.3 77.5 - - - +
994A HIS* 1.3 68.9 + - - +
995A PHE* 3.8 1.7 - - - -
1002A THR* 4.7 0.4 - - + -
1006A PRO* 4.5 5.8 - - + -
1076A TRP* 3.7 22.9 - - + -
1077A LEU 3.1 7.3 + - - -
1078A GLY* 3.3 6.2 - - - -
1079A LEU* 3.0 25.2 + - - -
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Residues in contact with HIS 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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903A PHE* 5.6 5.1 - - - -
993A ALA* 1.3 76.2 - - - +
995A PHE* 1.3 68.5 + - - +
1002A THR* 3.6 7.6 - - - +
1003A PHE* 3.2 47.8 + + + +
1004A GLY* 4.7 1.3 - - - -
1005A ILE* 3.6 35.1 + - - +
1007A PHE* 4.5 9.2 - + - -
1028A LEU* 5.2 13.9 - - + +
1038A PHE* 5.1 4.0 - + - -
1079A LEU* 3.6 27.0 - - + +
1081A HIS* 2.9 30.8 + + - +
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Residues in contact with PHE 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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993A ALA 3.8 0.7 - - - -
994A HIS* 1.3 76.7 - - - +
996A HIS* 1.3 54.5 + - - +
997A LYS* 2.9 52.9 - - + -
999A VAL* 5.4 0.2 - - + -
1001A GLY 3.6 4.5 - - - +
1002A THR* 4.1 2.2 - - + -
1003A PHE* 3.4 16.5 - - - -
1039A LYS 4.7 0.4 - - - -
1041A ALA* 4.2 15.9 - - + -
1043A VAL* 4.7 5.6 - - + -
1048A HIS* 5.5 0.9 - + - -
1050A TYR* 4.1 4.0 - + - -
1076A TRP* 3.8 13.9 - + - -
1078A GLY* 3.2 38.4 - - - -
1079A LEU 2.8 22.0 + - - +
1080A ASP* 3.2 37.0 - - + -
1081A HIS 2.7 35.0 + - - +
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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