Contacts of the strand formed by residues 992 - 998 (chain A) in PDB entry 3T06
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 992 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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956A PHE* 4.2 15.5 - - + -
959A LEU* 4.5 6.1 - - + -
964A ARG* 3.2 40.6 - - - +
987A LEU 3.7 0.7 - - - +
988A LEU* 3.7 1.1 - - - +
989A LEU* 2.8 40.7 + - + +
990A GLU 3.5 1.2 - - - -
991A ASP* 1.3 104.9 + - + +
993A LEU* 1.3 58.8 + - - +
994A VAL* 4.1 12.6 - - + -
1025A VAL* 4.2 14.1 - - + -
1026A LEU 3.4 4.5 - - - +
1027A LYS* 3.7 30.5 - - + -
1028A LEU* 3.8 5.8 - - - +
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Residues in contact with LEU 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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986A VAL* 3.9 20.0 - - + -
987A LEU 3.6 12.1 - - - +
988A LEU* 4.0 20.0 - - + -
992A LEU* 1.3 72.8 - - - +
994A VAL* 1.3 63.5 + - - +
995A LEU* 4.4 17.9 - - + +
1024A PRO 4.3 0.2 - - - +
1025A VAL* 3.7 2.9 - - - +
1026A LEU* 3.0 55.7 + - + +
1028A LEU* 4.1 13.5 - - + +
1045A ILE* 3.4 32.1 - - + -
1059A LEU* 4.8 4.3 - - + -
1070A TRP* 4.6 5.8 - - + -
1074A LEU* 4.6 7.0 - - + -
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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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959A LEU* 4.8 10.5 - - + -
961A LEU* 5.4 3.1 - - + -
986A VAL* 3.1 10.2 - - - +
987A LEU* 2.9 61.7 + - + +
989A LEU* 4.0 25.4 - - + -
992A LEU* 4.1 10.1 - - + -
993A LEU* 1.3 79.2 - - - +
995A LEU* 1.3 62.7 + - - +
996A LEU* 3.9 16.8 + - + -
1024A PRO 3.9 5.2 - - - +
1025A VAL* 4.6 13.7 - - + -
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Residues in contact with LEU 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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974A TRP* 4.3 14.4 - - + -
984A LEU* 3.6 25.5 - - + +
986A VAL* 3.6 33.0 - - + -
993A LEU* 4.4 17.7 - - + +
994A VAL* 1.3 74.9 - - - +
996A LEU* 1.3 63.6 - - - +
997A GLN 4.0 0.3 + - - -
1004A LEU 3.6 9.0 - - - +
1005A LEU* 3.9 8.4 - - - +
1006A LYS 5.2 0.3 + - - +
1023A SER 4.5 0.2 - - - +
1024A PRO* 3.1 34.0 + - + +
1026A LEU* 5.1 7.2 - - + -
1057A TYR* 4.1 33.2 - - + -
1059A LEU* 4.5 9.2 - - + -
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Residues in contact with LEU 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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936A TYR* 5.5 0.9 - - + -
940A LEU* 3.9 17.9 - - + -
959A LEU* 6.0 0.9 - - + -
961A LEU* 5.1 8.3 - - + -
984A LEU* 3.6 5.1 - - - -
985A HIS* 2.9 38.9 + - - +
987A LEU* 4.2 29.4 - - + -
994A VAL* 4.3 13.5 - - + -
995A LEU* 1.3 74.7 - - - +
997A GLN* 1.3 60.0 + - - +
998A LYS 4.1 0.2 + - - -
1003A LEU* 3.9 42.0 - - + -
1004A LEU 3.4 6.5 - - - +
1005A LEU* 3.5 32.3 - - + -
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Residues in contact with GLN 997 (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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982A LEU* 4.0 24.5 - - + +
983A ASP* 3.7 26.5 + - - +
984A LEU* 4.5 7.6 - - + -
995A LEU 4.0 0.6 + - - -
996A LEU* 1.3 73.4 - - - +
998A LYS* 1.3 70.3 + - - +
999A GLN* 3.1 12.6 + - - +
1003A LEU* 3.8 3.2 - - - -
1004A LEU* 3.3 43.5 + - + +
1006A LYS* 4.3 17.5 + - + +
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Residues in contact with LYS 998 (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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936A TYR* 5.7 4.0 + - - -
939A ARG* 3.8 34.7 - - - +
983A ASP 4.6 2.8 + - - -
984A LEU* 5.4 0.6 - - - +
985A HIS* 4.3 37.5 + - + +
996A LEU 4.1 2.0 + - - -
997A GLN* 1.3 79.9 + - - +
999A GLN* 1.3 67.7 + - - +
1000A ASP 4.4 8.3 - - - +
1002A LYS 3.8 5.2 - - - +
1003A LEU* 4.2 10.0 - - + +
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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