Contacts of the strand formed by residues 648 - 652 (chain A) in PDB entry 1QWN
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 SER 648 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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646A TYR 3.8 1.2 + - - -
647A ALA* 1.3 75.5 - - - +
649A ASN* 1.3 64.1 + - - +
666A GLU* 3.2 30.3 - - - -
669A LYS* 6.3 1.1 - - - -
747A VAL 4.5 0.4 - - - -
748A THR* 3.3 4.7 - - - +
749A LYS* 2.8 53.4 + - - +
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Residues in contact with ASN 649 (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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594A PRO* 3.4 26.6 - - - +
596A TRP* 3.1 29.1 + - + -
647A ALA 3.5 13.1 + - - -
648A SER* 1.3 81.3 + - - +
650A LEU* 1.3 60.9 + - - +
651A LEU 4.3 0.4 - - - -
661A LEU* 4.6 2.4 - - - +
664A TYR* 3.6 9.7 + - - -
666A GLU* 4.7 2.4 + - - +
667A ASP 4.4 2.0 + - - +
668A VAL* 3.6 15.5 - - + +
669A LYS* 2.8 30.3 + - - +
746A LEU* 4.6 2.2 - - + -
747A VAL 3.4 4.5 - - - +
748A THR* 2.8 29.3 + - - +
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Residues in contact with LEU 650 (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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649A ASN* 1.3 74.7 - - - +
651A LEU* 1.3 57.9 + - - +
652A LEU* 3.7 28.0 - - + -
669A LYS* 3.3 30.7 - - + +
670A PHE 3.8 17.9 - - - +
674A ARG* 3.4 31.4 - - - +
676A ILE* 5.2 3.8 - - + -
745A VAL 3.7 1.2 - - - +
746A LEU* 3.5 5.2 - - - +
747A VAL* 2.8 53.6 + - + +
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Residues in contact with LEU 651 (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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609A PRO* 3.6 30.7 - - + -
649A ASN 4.3 0.4 - - - -
650A LEU* 1.3 72.5 - - - +
652A LEU* 1.3 58.7 + - - +
653A ARG* 3.2 35.9 + - + +
656A PRO* 5.1 0.7 - - + -
659A LEU* 3.9 22.2 - - + -
668A VAL* 4.5 2.0 - - + +
669A LYS 2.8 10.0 + - - +
670A PHE* 3.3 25.6 - - + +
671A GLY 3.1 21.8 + - - +
744A VAL* 3.7 20.4 - - + -
745A VAL 3.7 7.9 - - - +
746A LEU* 4.1 12.6 - - + -
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Residues in contact with LEU 652 (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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650A LEU* 3.7 28.9 - - + +
651A LEU* 1.3 70.5 - - - +
653A ARG* 1.3 65.3 + - - +
671A GLY* 3.2 18.2 - - - +
672A ASP 3.6 15.9 - - - +
673A PRO* 4.1 15.1 - - + +
674A ARG* 3.9 35.9 - - + +
676A ILE* 4.2 14.4 - - + -
690A GLU 6.1 0.4 - - - +
743A PRO 4.1 2.6 - - - +
744A VAL* 3.7 2.6 - - - +
745A VAL* 2.8 46.9 + - + +
747A VAL* 4.2 15.0 - - + -
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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