Contacts of the strand formed by residues 1057 - 1061 (chain D) in PDB entry 6K4Y
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 SER1057 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1048D ARG* 3.4 35.2 - - - +
1049D GLN 4.6 0.7 - - - -
1050D THR* 4.7 1.6 - - - +
1055D GLY 3.8 1.4 + - - -
1056D LEU* 1.3 73.5 - - - +
1058D SER* 1.3 59.9 + - - +
1059D LEU* 3.7 2.2 - - - +
1107D VAL 3.5 9.5 - - - +
1108D GLN* 2.9 20.7 + - - +
1110D GLU* 2.6 37.6 + - - +
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Residues in contact with SER1058 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1048D ARG* 5.0 0.6 - - - +
1049D GLN* 2.8 49.1 + - - +
1051D ASP* 2.4 33.0 + - - -
1056D LEU 3.4 0.4 + - - -
1057D SER* 1.3 71.9 - - - +
1059D LEU* 1.3 61.3 + - - +
1060D VAL* 3.1 12.9 + - - +
1106D ILE* 3.7 20.1 - - - +
1107D VAL 3.6 4.9 - - - -
1108D GLN* 3.6 11.8 + - - -
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Residues in contact with LEU1059 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037D PHE* 3.6 35.9 - - + -
1042D ASP* 3.4 33.7 - - + +
1046D ILE* 3.7 20.9 - - + +
1047D THR 3.4 6.1 - - - +
1048D ARG* 3.4 32.1 - - - +
1057D SER* 3.7 2.9 - - - +
1058D SER* 1.3 67.1 - - - +
1060D VAL* 1.3 60.5 + - - +
1061D VAL* 3.8 0.7 + - - +
1107D VAL* 2.8 49.5 + - + +
1110D GLU* 4.6 12.1 - - + +
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Residues in contact with VAL1060 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046D ILE* 4.3 1.1 - - - -
1047D THR* 2.9 37.2 + - + +
1049D GLN* 3.3 39.0 - - + +
1058D SER* 3.1 18.1 + - - +
1059D LEU* 1.3 72.3 - - - +
1061D VAL* 1.3 73.3 + - - +
1062D LEU* 5.4 2.5 - - + -
1104D LYS* 4.3 8.1 - - - +
1105D ALA 3.0 17.5 - - - +
1106D ILE* 3.8 26.2 - - + +
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Residues in contact with VAL1061 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1040D MET* 5.0 0.2 - - + -
1045D THR 4.4 0.4 - - - +
1046D ILE* 3.7 23.6 - - + +
1060D VAL* 1.3 75.9 - - - +
1062D LEU* 1.3 70.8 + - - +
1067D ARG* 3.4 13.9 - - - +
1076D PRO* 3.7 12.8 - - + -
1101D LEU* 3.4 45.3 - - + +
1102D PRO 3.4 18.2 - - - +
1103D GLY* 3.3 0.9 - - - -
1104D LYS 3.3 24.3 + - - -
1105D ALA* 2.9 10.6 + - + +
1107D VAL* 4.3 5.6 - - + -
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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