Contacts of the strand formed by residues 962 - 970 (chain A) in PDB entry 3KHF
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 PHE 962 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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953A ILE* 4.6 2.9 - - + -
960A TYR* 3.8 26.7 - + + -
961A GLY* 1.3 79.2 - - - +
963A SER* 1.3 72.5 + - - +
964A LEU* 4.4 10.3 - - + -
983A VAL* 4.2 5.4 - - + -
985A SER* 3.2 15.3 - - - +
986A VAL* 4.1 5.6 - - + +
987A GLU* 4.7 2.2 - - - +
992A ALA* 3.8 6.1 - - + -
997A LEU* 3.5 33.0 - - + -
1003A ILE* 4.0 20.4 - - + -
1023A LEU* 4.1 19.3 - - + -
1030A ILE* 6.0 0.4 - - + -
1032A LEU* 4.3 14.8 - - + -
1043B SER* 3.5 3.0 - - - -
1044B VAL* 2.8 54.2 + - + +
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Residues in contact with SER 963 (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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962A PHE* 1.3 76.7 - - - +
964A LEU* 1.3 63.8 + - - +
983A VAL* 3.4 6.2 - - - +
984A TRP* 2.8 22.1 + - - +
985A SER* 2.7 32.1 + - - +
1041B GLU* 2.6 35.2 + - - +
1042B THR 3.2 12.3 - - - -
1043B SER* 3.8 13.9 - - - -
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Residues in contact with LEU 964 (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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962A PHE* 4.4 4.7 - - + -
963A SER* 1.3 76.9 - - - +
965A ARG* 1.3 65.3 + - - +
981A HIS* 4.2 19.1 - - + +
982A VAL 3.3 16.4 - - - +
983A VAL* 4.2 2.9 - - + -
984A TRP 4.1 1.3 - - - +
1003A ILE* 4.2 13.7 - - + -
1016A HIS* 3.8 19.2 - - + -
1019A VAL* 4.0 26.5 - - + -
1020A VAL* 4.7 3.1 - - + -
1023A LEU* 4.1 21.3 - - + -
1041B GLU* 3.4 3.3 - - - -
1042B THR* 2.9 44.5 + - - +
1044B VAL* 4.2 14.4 - - + -
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Residues in contact with ARG 965 (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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964A LEU* 1.3 78.0 - - - +
966A ALA* 1.3 59.9 + - - +
967A ILE* 3.8 10.7 + - + -
980A HIS 3.5 1.4 - - - +
981A HIS* 3.5 4.0 - - - -
982A VAL* 2.9 31.9 + - - +
984A TRP* 3.4 51.3 - - + -
1016A HIS* 4.5 2.9 - - - -
999B ALA* 3.5 30.7 + - - +
1000B GLY* 3.8 9.6 - - - -
1038B GLU* 4.7 6.3 + - - -
1039B ASN 2.7 34.0 + - - +
1040B THR* 3.5 15.7 - - - +
1041B GLU* 3.5 43.0 + - + +
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Residues in contact with ALA 966 (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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965A ARG* 1.3 71.1 - - - +
967A ILE* 1.3 61.4 + - - +
968A ARG* 5.0 1.8 - - + +
979A VAL* 3.7 20.6 - - + -
980A HIS 3.4 6.5 - - - -
981A HIS* 4.2 4.0 - - - +
1016A HIS* 3.5 40.8 + - + +
1039B ASN* 3.2 25.6 - - - +
1040B THR 4.1 4.2 + - - +
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Residues in contact with ILE 967 (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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965A ARG* 3.9 7.9 - - + +
966A ALA* 1.3 74.0 - - - +
968A ARG* 1.3 68.6 + - - +
969A VAL* 3.3 19.7 + - + +
979A VAL* 3.5 2.6 - - - -
980A HIS* 2.7 45.9 + - + +
982A VAL* 4.1 18.8 - - + -
984A TRP* 3.8 27.1 - - + -
967B ILE* 4.6 2.5 - - + -
982B VAL* 4.1 20.9 - - + -
1000B GLY* 3.5 20.2 - - - +
1002B LEU* 4.4 7.4 - - + -
1039B ASN* 3.8 20.4 - - + +
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Residues in contact with ARG 968 (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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966A ALA 5.0 2.2 - - - +
967A ILE* 1.3 72.3 - - - +
969A VAL* 1.3 60.8 + - - +
970A TYR* 3.4 43.9 + - + -
977A TYR* 3.9 39.7 + - + -
978A THR 4.2 2.7 - - - -
979A VAL* 4.8 5.8 - - + +
1002B LEU* 3.8 10.6 - - - +
1035B THR* 5.0 0.5 + - - +
1037B LEU* 3.6 32.7 + - - +
1038B GLU 3.4 21.0 + - - -
1039B ASN* 3.0 33.0 + - - +
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Residues in contact with VAL 969 (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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967A ILE* 3.8 17.5 - - + +
968A ARG* 1.3 73.0 - - - +
970A TYR* 1.3 65.2 + - - +
977A TYR* 3.2 5.2 - - - +
978A THR* 3.1 34.7 + - - +
980A HIS* 3.3 32.5 - - + +
967B ILE* 4.9 0.9 - - + -
969B VAL* 3.9 24.0 - - + -
970B TYR 4.9 0.2 - - - +
971B MET* 3.7 28.9 - - + +
980B HIS* 4.3 11.0 - - + -
1002B LEU* 4.1 6.7 - - + -
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Residues in contact with TYR 970 (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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968A ARG* 3.4 42.5 - - + -
969A VAL* 1.3 86.6 - - - +
971A MET* 1.3 59.8 + - - +
972A GLY 3.9 13.9 - - - +
974A SER 3.5 19.1 - - - +
975A ASP* 4.2 13.7 + - - -
976A VAL 3.3 22.4 - - - +
977A TYR* 3.7 23.2 - + - -
971B MET* 4.2 4.1 - - - +
980B HIS* 4.4 12.0 + - - -
1002B LEU* 3.8 8.8 - - + +
1004B THR* 5.7 4.7 - - + -
1012B LEU* 5.1 1.4 - - - +
1035B THR* 3.7 31.5 - - + -
1037B LEU* 4.9 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