Contacts of the strand formed by residues 423 - 431 (chain A) in PDB entry 4WGK
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 LEU 423 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A TYR* 3.5 28.3 - - + -
144A MET* 3.7 13.0 - - + +
145A ALA* 3.6 36.8 - - - +
146A GLU* 2.9 18.1 + - - +
151A ASN* 3.3 42.2 + - + +
153A THR* 4.1 8.7 - - + +
422A PRO* 1.3 76.8 - - - +
424A ALA* 1.3 64.0 + - - +
528A THR 3.4 2.2 - - - +
529A LEU* 3.7 35.7 - - + -
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Residues in contact with ALA 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A THR* 4.2 4.6 - - - +
422A PRO* 5.2 2.7 - - + +
423A LEU* 1.3 76.5 - - - +
425A SER* 1.3 64.8 + - - +
527A ILE* 3.5 4.0 - - - +
528A THR* 2.8 44.9 + - - +
617A ILE* 3.7 23.3 - - + +
622A VAL* 6.3 1.8 - - + -
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Residues in contact with SER 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A THR* 4.9 3.0 - - - +
184A ARG* 4.3 2.3 + - - -
186A ASP* 2.9 44.8 + - - +
187A ASN* 3.7 11.0 - - - +
424A ALA* 1.3 79.2 - - - +
426A ALA* 1.3 63.1 + - - +
526A ILE 3.3 7.0 - - - -
527A ILE* 3.8 12.1 - - - -
617A ILE* 4.3 4.9 - - - +
622A VAL* 4.2 17.7 - - - +
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Residues in contact with ALA 426 (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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186A ASP* 4.6 3.4 - - - -
425A SER* 1.3 74.9 - - - +
427A HIS* 1.3 61.9 + - - +
525A GLN* 3.1 5.9 - - - +
526A ILE 3.0 32.2 + - - +
613A LEU* 4.1 14.3 - - + +
617A ILE* 3.6 25.1 - - + +
622A VAL* 4.3 9.6 - - + -
625A LEU* 4.0 22.2 - - + -
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Residues in contact with HIS 427 (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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168A ARG* 3.8 7.6 + - - -
185A ARG* 3.5 41.1 + - + -
186A ASP* 3.5 27.4 - - + +
426A ALA* 1.3 76.7 - - - +
428A GLN* 1.3 83.4 + - - +
429A TRP* 3.5 23.8 - + - -
523A ASP* 2.7 37.1 + - + +
524A VAL 3.5 13.2 - - - -
525A GLN* 3.8 11.4 - - + -
613A LEU* 4.9 2.2 - - - -
625A LEU* 4.5 12.1 - - - +
626A SER 5.0 1.4 - - - +
627A ARG* 5.2 2.5 + - - +
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Residues in contact with GLN 428 (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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427A HIS* 1.3 88.1 + - - +
429A TRP* 1.3 72.3 + - - +
430A VAL* 4.4 10.4 - - + +
522A VAL 3.8 0.3 - - - +
524A VAL* 3.0 43.8 + - + +
609A LEU* 4.7 8.1 - - - +
612A ASN* 4.3 10.3 + - - +
613A LEU* 3.7 19.9 - - + +
625A LEU* 4.3 12.8 - - + +
626A SER* 3.0 49.9 + - - +
627A ARG 4.0 3.6 - - - -
628A GLY* 5.0 0.4 - - - -
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Residues in contact with TRP 429 (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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165A GLN* 5.4 0.6 + - - -
168A ARG* 5.7 0.2 - - - +
169A LEU* 5.3 9.0 - - + +
172A LEU* 6.3 1.6 - - + -
185A ARG* 3.2 36.8 - - + -
427A HIS* 3.5 9.5 - + - -
428A GLN* 1.3 75.7 - - - +
430A VAL* 1.3 64.1 + - - +
521A ILE* 4.0 8.3 - - + -
522A VAL 3.7 2.2 - - - -
523A ASP* 2.9 33.2 + - - -
627A ARG* 3.1 45.2 + - + +
628A GLY* 3.2 36.2 - - - -
629A PRO* 3.2 22.2 - - - +
630A GLU* 3.9 24.5 - - + -
631A PRO* 3.4 31.3 - - + +
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Residues in contact with VAL 430 (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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428A GLN* 4.2 9.4 - - + +
429A TRP* 1.3 80.4 - - - +
431A ASP* 1.3 62.5 + - - +
432A MET* 3.1 14.3 + - + -
435A VAL* 3.8 21.8 - - + -
520A ASP 3.3 0.2 - - - +
521A ILE* 3.5 3.5 - - - +
522A VAL* 2.9 40.9 + - - +
524A VAL* 3.8 28.9 - - + -
609A LEU* 3.7 36.6 - - + -
629A PRO* 4.7 1.6 - - - -
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Residues in contact with ASP 431 (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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430A VAL* 1.3 70.7 - - - +
432A MET* 1.3 58.5 + - - +
433A THR* 2.6 41.0 + - - +
434A ASP* 3.2 21.9 + - + +
435A VAL* 3.3 12.6 + - - +
520A ASP* 3.5 11.1 - - - +
521A ILE* 4.1 17.2 - - + +
629A PRO* 4.2 13.6 - - + +
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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