Contacts of the strand formed by residues 977 - 984 (chain A) in PDB entry 6M0X
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 LYS 977 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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971A PHE* 3.6 5.4 - - - -
972A ASN* 3.0 29.5 + - - +
975A THR* 3.2 34.7 + - + +
976A GLY* 1.3 78.5 - - - +
978A TYR* 1.3 66.8 + - - +
979A GLU* 4.9 2.0 - - + -
1090A GLY 3.4 26.2 - - - +
1091A LYS* 4.0 4.5 - - - +
1092A SER* 3.7 35.7 - - - +
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Residues in contact with TYR 978 (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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969A VAL* 4.1 13.7 - - + -
970A TYR 3.3 19.7 - - - +
971A PHE* 3.6 27.5 - + - -
977A LYS* 1.3 78.8 - - - +
979A GLU* 1.3 63.9 + - - +
980A ILE* 4.3 7.6 - - + -
1020A LYS* 4.0 22.4 + - - -
1054A HIS* 3.8 4.9 + - - -
1089A LEU 3.7 14.9 + - - +
1090A GLY* 3.4 20.4 - - - -
1091A LYS 4.8 0.8 + - - -
1094A ILE* 3.3 38.6 - - + -
1095A SER* 4.0 3.8 - - - -
1096A ILE* 3.5 47.6 + - + -
1097A TYR* 4.5 7.3 - - - -
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Residues in contact with GLU 979 (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 TYR* 2.9 42.5 + - + +
972A ASN* 3.1 28.5 + - + +
975A THR* 5.0 2.2 + - - +
977A LYS* 4.4 7.4 - - + +
978A TYR* 1.3 80.0 - - - +
980A ILE* 1.3 61.2 + - - +
1012A GLY 3.3 17.3 - - - +
1013A VAL* 3.6 15.6 - - + -
1014A ASP* 3.0 20.7 + - - +
1017A SER* 3.2 19.1 + - - -
1054A HIS* 3.3 19.4 + - + +
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Residues in contact with ILE 980 (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 ALA* 3.7 27.1 - - + -
968A ASP 3.5 7.0 - - - +
969A VAL* 4.4 23.8 - - + -
978A TYR* 4.9 3.8 - - + -
979A GLU* 1.3 79.3 - - - +
981A LEU* 1.3 62.7 + - - +
1011A GLU* 3.5 17.5 - - - +
1013A VAL* 4.2 3.5 - - - +
1023A LEU* 5.7 3.1 - - + -
1044A PHE* 5.6 0.4 - - + -
1047A ARG* 3.8 11.9 + - - -
1054A HIS* 3.3 28.7 - - + +
1056A VAL* 4.0 26.7 - - + -
1089A LEU* 4.0 30.5 - - + +
1096A ILE* 4.9 5.6 - - + -
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Residues in contact with LEU 981 (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 ALA* 3.0 6.1 - - - +
968A ASP* 2.7 49.6 + - + +
970A TYR* 4.1 5.6 - - + -
979A GLU 4.0 0.8 + - - -
980A ILE* 1.3 74.3 - - - +
982A GLY* 1.3 60.9 + - - +
983A LEU* 3.9 27.1 - - + -
1004A TYR* 3.5 36.1 - - + +
1007A ILE* 3.9 22.0 - - + +
1008A LYS* 3.6 38.8 - - + +
1011A GLU* 4.1 6.5 - - + -
1013A VAL* 4.0 9.9 - - + -
1047A ARG* 4.8 0.2 - - - -
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Residues in contact with GLY 982 (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 ARG 3.7 4.9 - - - -
980A ILE 4.0 0.4 + - - -
981A LEU* 1.3 77.1 - - - +
983A LEU* 1.3 61.2 + - - +
984A LYS* 4.2 5.0 + - - +
987A ASP* 4.3 2.8 - - - +
1007A ILE* 3.8 15.8 - - - +
1011A GLU* 3.0 22.1 + - - +
1047A ARG* 3.7 23.1 - - - +
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Residues in contact with LEU 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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964A PRO* 3.7 4.7 - - - +
965A TRP* 2.7 48.9 + - + -
966A ARG* 2.7 54.1 + - + +
968A ASP* 4.3 1.1 - - - +
981A LEU* 3.9 19.7 + - + -
982A GLY* 1.3 73.4 - - - -
984A LYS* 1.3 56.0 + - - +
987A ASP* 3.8 4.9 - - + +
988A LEU* 5.1 0.4 - - + -
999A ILE* 3.8 20.4 - - + -
1004A TYR* 4.0 21.1 - - + -
1007A ILE* 3.7 28.3 - - + -
1119A LEU* 4.8 3.4 - - + -
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Residues in contact with LYS 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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944A ASN* 4.1 19.3 - - - +
962A VAL* 2.6 48.5 + - + -
963A SER 3.2 11.0 - - - +
964A PRO* 4.0 19.1 - - + +
965A TRP* 3.6 5.4 - - - +
982A GLY 5.0 4.7 - - - +
983A LEU* 1.3 79.7 - - - +
985A TYR* 1.3 69.0 + - - +
986A ALA* 3.1 6.3 - - + +
987A ASP* 2.9 33.1 + - - +
988A LEU* 4.0 7.3 + - - +
1047A ARG 4.9 8.0 + - - -
1050A PRO* 5.0 10.3 - - - +
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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