Contacts of the strand formed by residues 982 - 992 (chain A) in PDB entry 1K3A
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 MET 982 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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974A GLU* 3.4 35.9 - - - +
976A GLY* 3.4 25.8 - - - +
977A GLN* 3.4 32.0 + - + +
981A GLY* 1.3 71.3 - - - -
983A VAL* 1.3 66.1 + - - +
984A TYR* 3.4 39.2 - - + +
1004A THR* 2.8 40.5 + - - +
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Residues in contact with VAL 983 (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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300A ACP 3.4 56.5 - - + +
974A GLU* 3.8 0.2 - - - -
975A LEU* 2.8 27.3 + - + -
976A GLY 2.8 22.0 + - - +
978A GLY* 4.1 4.5 - - - +
981A GLY 4.0 9.2 - - - +
982A MET* 1.3 79.6 - - - +
984A TYR* 1.3 68.7 + - - +
1001A ALA* 4.8 0.4 - - + -
1002A ILE 3.3 16.2 - - - +
1003A LYS* 4.2 21.5 - - + -
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Residues in contact with TYR 984 (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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971A MET* 3.3 44.4 - - + -
973A ARG* 3.3 10.5 - - - +
974A GLU* 3.7 34.6 + - + -
975A LEU* 3.8 7.5 - - - +
982A MET* 3.4 32.0 - - + +
983A VAL* 1.3 73.9 - - - +
985A GLU* 1.3 65.1 + - - +
1001A ALA* 3.4 3.3 - - - -
1002A ILE* 2.5 45.4 + - + +
1004A THR* 3.6 26.9 + - + -
1044A PRO* 6.4 0.2 - - + -
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Residues in contact with GLU 985 (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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971A MET* 3.8 2.3 - - - -
972A SER* 2.9 26.4 + - - -
973A ARG* 2.7 58.7 + - + +
975A LEU* 3.7 20.5 - - + +
984A TYR* 1.3 75.0 - - - +
986A GLY* 1.3 64.0 + - - +
999A ARG* 2.9 34.5 + - - -
1000A VAL 3.5 3.6 - - - +
1002A ILE* 4.5 1.1 - - - -
1051A LEU* 3.8 25.1 - - + +
1053A THR* 5.8 0.9 - - - +
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Residues in contact with GLY 986 (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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970A THR 3.1 15.0 - - - -
972A SER* 3.7 9.4 - - - -
984A TYR 4.1 0.6 + - - -
985A GLU* 1.3 81.5 - - - +
987A VAL* 1.3 69.9 + - - +
999A ARG* 3.5 4.3 - - - +
1000A VAL* 2.9 32.0 + - - +
1002A ILE* 4.0 5.7 - - - +
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Residues in contact with VAL 987 (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 LYS 3.8 1.3 - - - +
969A ILE* 3.4 3.1 - - - +
970A THR* 2.9 45.0 + - - +
972A SER* 4.7 7.2 - - - +
986A GLY* 1.3 80.2 - - - +
988A ALA* 1.3 65.4 + - - +
989A LYS* 5.3 5.2 - - + +
997A GLU* 3.6 42.0 - - + +
998A THR 3.3 9.2 - - - +
999A ARG* 4.7 11.9 - - + -
1000A VAL* 3.9 3.1 - - - +
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Residues in contact with ALA 988 (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 LYS 3.2 5.2 - - - -
969A ILE* 4.0 20.4 - - + -
987A VAL* 1.3 76.2 - - - +
989A LYS* 1.3 63.1 + - - +
990A GLY 4.1 0.2 + - - -
991A VAL* 4.0 11.6 - - + +
997A GLU* 3.2 1.7 - - - -
998A THR* 2.7 39.3 + - - -
1000A VAL* 4.0 21.8 - - + -
1048A ILE* 4.0 13.7 - - + -
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Residues in contact with LYS 989 (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 VAL* 6.1 0.3 - - - +
968A LYS* 2.9 50.9 + - + +
970A THR* 5.7 7.5 - - - +
987A VAL* 5.3 4.2 - - + +
988A ALA* 1.3 75.1 - - - +
990A GLY* 1.3 65.4 + - - +
991A VAL* 3.4 7.6 + - - +
996A PRO 3.4 11.0 - - - +
997A GLU* 4.0 23.6 + - + -
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Residues in contact with GLY 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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968A LYS* 5.8 0.7 - - - -
988A ALA 4.1 0.6 + - - -
989A LYS* 1.3 72.7 - - - +
991A VAL* 1.3 61.5 + - - +
992A VAL 3.5 4.0 - - - -
995A GLU 4.1 7.4 + - - -
996A PRO* 2.8 18.2 + - - -
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Residues in contact with VAL 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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964A VAL* 4.4 14.1 - - + -
969A ILE* 5.6 0.9 - - + -
988A ALA* 4.0 18.1 + - + +
989A LYS 3.9 9.2 - - - +
990A GLY* 1.3 79.2 - - - +
992A VAL* 1.3 69.6 + - + +
995A GLU 4.7 0.6 + - - -
998A THR* 3.7 26.9 + - - +
1036A LEU* 4.0 35.0 - - + +
1048A ILE* 3.6 25.4 - - + -
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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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990A GLY* 4.6 2.4 - - - -
991A VAL* 1.3 89.3 + - + +
993A LYS* 1.3 77.1 + - + +
994A ASP 3.6 0.2 + - - -
995A GLU* 3.1 41.8 + - + +
998A THR* 3.6 27.9 + - + +
1036A LEU* 4.0 21.3 - - + -
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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