Contacts of the strand formed by residues 993 - 999 (chain K) in PDB entry 6R90
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 GLN 993 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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950K ASN* 5.6 0.4 - - - +
977K CYS* 3.3 17.2 - - - -
978K GLN* 3.2 8.0 + - + +
979K LYS 5.7 0.2 - - - -
980K ASP* 4.6 21.7 + - + +
991K HIS* 3.5 31.6 + - - +
992K LEU* 1.3 88.3 + - - +
994K GLU* 1.3 61.1 + - - +
995K VAL* 2.9 28.1 + - + +
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Residues in contact with GLU 994 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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948K ASP* 5.3 0.8 - - - +
950K ASN* 3.1 42.4 + - - +
952K ASN* 4.9 6.6 + - - +
975K PHE* 4.9 7.2 - - + +
976K VAL 3.7 6.7 - - - +
977K CYS* 3.9 13.5 - - - -
992K LEU 4.2 0.4 + - - -
993K GLN* 1.3 69.1 - - - +
995K VAL* 1.3 61.5 + - - +
996K GLY 3.4 4.1 + - - +
997K LEU* 3.8 34.7 - - + +
1076K PHE* 5.4 2.6 - - - -
1081K LYS* 3.4 22.8 + - - -
1083K GLU* 5.1 0.9 - - - +
1086K THR* 5.3 1.4 - - - +
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Residues in contact with VAL 995 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K MET* 3.4 29.2 - - + +
2K SER* 4.5 13.1 - - - +
976K VAL* 2.9 8.8 + - - +
978K GLN* 4.5 22.2 - - + +
993K GLN* 3.2 28.5 - - + +
994K GLU* 1.3 75.0 - - - +
996K GLY* 1.3 57.0 + - - +
1086K THR* 3.5 19.4 + - - +
1087K GLY* 4.4 5.2 - - - -
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Residues in contact with GLY 996 (chain K).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2K SER 5.5 1.3 - - - -
975K PHE* 3.1 9.9 - - - +
976K VAL* 2.9 40.8 + - - +
994K GLU 3.4 0.7 - - - -
995K VAL* 1.3 80.8 + - - +
997K LEU* 1.3 66.3 + - - +
1086K THR* 3.3 10.5 - - - -
1087K GLY* 4.3 5.2 - - - -
1088K PHE* 4.2 5.6 - - - -
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Residues in contact with LEU 997 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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974K LEU 3.4 3.8 - - - +
975K PHE* 3.4 20.2 - - + +
994K GLU* 3.8 30.1 - - + +
996K GLY* 1.3 83.7 - - - +
998K PHE* 1.3 63.9 + - - +
1076K PHE* 3.5 41.7 - - + -
1081K LYS* 5.4 0.4 - - - +
1083K GLU* 3.0 40.8 - - - +
1084K PRO 4.8 1.3 - - - +
1085K ALA* 3.5 4.1 - - - +
1086K THR* 2.7 46.1 + - + +
1088K PHE* 3.9 2.6 - - - +
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Residues in contact with PHE 998 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K VAL* 5.4 8.7 - - + -
973K ASN* 3.2 5.7 - - - -
974K LEU* 2.8 44.8 + - + +
997K LEU* 1.3 76.3 - - - +
999K HIS* 1.3 72.6 + - - +
1000K LEU* 3.3 26.0 + - + -
1055K GLN* 6.1 0.2 - - - -
1074K ARG* 3.6 43.7 - - + -
1076K PHE* 4.6 3.6 - - - +
1085K ALA* 4.4 16.2 - - + -
1088K PHE* 3.6 42.2 - + + -
1089K ILE 4.9 1.3 - - - -
1090K ASP* 4.1 28.3 - - + -
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Residues in contact with HIS 999 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60K LYS* 5.3 5.1 - - + +
83K LYS* 3.5 24.0 + - + -
971K ALA 3.8 11.9 + - - -
972K PHE* 3.1 27.1 - + - +
973K ASN* 3.2 19.8 + - - +
998K PHE* 1.3 80.0 - - - +
1000K LEU* 1.3 62.0 + - - +
1001K GLY* 3.2 24.7 - - - -
1073K TRP* 3.4 25.1 + + - +
1074K ARG* 3.3 32.1 + - - +
1075K SER 3.3 22.5 + - - +
1076K PHE 4.6 1.4 - - - +
1077K HIS* 4.6 6.2 - + + +
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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