Contacts of the strand formed by residues 1009 - 1013 (chain A) in PDB entry 4E5W
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 VAL1009 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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963A SER* 3.1 4.3 - - - -
964A LEU* 2.8 49.7 + - + -
987A ILE* 4.0 24.5 - - + -
1004A LEU* 4.2 19.7 - - + -
1005A ALA 3.6 17.3 - - - +
1006A ALA* 3.2 8.7 + - - +
1007A ARG 3.5 0.2 - - - -
1008A ASN* 1.3 80.7 - - - +
1010A LEU* 1.3 61.5 + - - +
1017A VAL* 3.7 23.3 - - + -
1018A LYS 3.6 9.6 - - - +
1019A ILE* 5.0 6.3 - - + -
1070A THR* 4.5 1.8 - - + -
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Residues in contact with LEU1010 (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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938A VAL* 3.9 15.0 - - + -
959A LEU* 3.6 20.6 - - + -
962A GLY 3.3 9.9 - - - +
963A SER* 4.2 2.0 - - - -
1008A ASN 4.9 1.1 - - - +
1009A VAL* 1.3 75.9 - - - +
1011A VAL* 1.3 61.9 + - - +
1012A GLU 3.9 0.2 - - - -
1017A VAL* 3.1 9.3 - - - +
1018A LYS* 2.7 36.4 + - + +
1020A GLY* 3.7 26.9 - - - -
1201A 0NT 3.5 79.0 - - + +
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Residues in contact with VAL1011 (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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959A LEU* 3.8 15.4 - - - +
960A PRO* 5.7 0.3 - - - +
961A SER* 3.5 30.8 + - - -
962A GLY 2.8 16.2 + - - +
964A LEU* 3.7 29.2 - - + +
967A TYR* 3.7 44.4 - - + -
983A TYR* 4.8 2.5 - - - +
1010A LEU* 1.3 71.2 - - - +
1012A GLU* 1.3 60.6 + - - +
1013A SER* 3.2 27.8 - - - +
1016A GLN 3.8 3.1 - - - +
1017A VAL* 4.3 2.7 - - + -
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Residues in contact with GLU1012 (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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957A GLU* 4.4 3.7 - - - +
959A LEU* 3.5 31.9 - - + +
960A PRO* 5.9 2.9 - - - +
961A SER* 5.1 2.9 + - - -
1010A LEU 3.8 1.4 + - - -
1011A VAL* 1.3 74.3 - - - +
1013A SER* 1.3 62.4 + - - +
1016A GLN* 2.8 49.9 + - + +
1018A LYS* 3.6 23.2 + - + -
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Residues in contact with SER1013 (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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961A SER* 5.4 3.1 - - - -
967A TYR* 4.8 0.4 - - - -
983A TYR* 4.1 1.7 + - - -
1011A VAL* 3.2 17.3 - - - +
1012A GLU* 1.3 81.0 - - - +
1014A GLU* 1.3 64.3 + - - +
1015A HIS* 3.0 23.9 + - - +
1016A GLN* 3.1 28.9 + - - +
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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