Contacts of the strand formed by residues 425 - 432 (chain E) in PDB entry 4G3D
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 425 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402E HIS* 5.8 2.7 - - - +
416E ARG* 3.8 31.4 - - + +
417E MET 3.3 13.5 - - - +
418E GLU* 3.7 27.6 - - + +
423E GLY 3.7 4.7 + - - +
424E PHE* 1.3 89.0 - - - +
426E CYS* 1.3 62.4 + - - +
471E LEU* 4.8 10.3 + - + +
473E GLU* 5.7 2.2 + - - -
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Residues in contact with CYS 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386E LEU* 4.2 13.5 - - - -
416E ARG* 3.7 4.5 - - - +
417E MET* 3.0 58.1 + - - -
424E PHE* 3.7 14.3 + - + -
425E GLN* 1.3 75.1 - - - +
427E ALA* 1.3 69.0 + - - +
456E TYR* 3.8 14.1 - - + -
468E PHE* 4.4 7.4 - - - -
469E MET 3.1 15.0 - - - +
471E LEU* 3.7 18.0 - - - +
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Residues in contact with ALA 427 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414E VAL* 4.7 11.9 - - + -
415E HIS 3.3 12.8 - - - +
417E MET* 4.2 1.8 - - - -
426E CYS* 1.3 83.8 - - - +
428E VAL* 1.3 62.9 + - - +
467E ILE 3.7 0.3 - - - +
468E PHE* 3.3 5.5 - - - +
469E MET* 2.8 46.3 + - + +
470E GLU 4.4 0.7 - - - +
471E LEU* 4.0 24.9 - - + +
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Residues in contact with VAL 428 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399E TRP* 3.7 24.7 - - + -
401E THR* 4.2 8.7 - - + -
413E GLU 3.5 0.9 - - - +
414E VAL* 3.0 10.3 - - - +
415E HIS* 3.0 38.5 + - + +
417E MET* 3.3 35.7 - - + -
427E ALA* 1.3 74.1 - - - +
429E LYS* 1.3 65.8 + - - +
430E LYS* 3.9 3.8 - - + +
466E ASN* 4.1 13.9 - - + +
467E ILE 3.2 8.3 - - - +
468E PHE* 3.6 21.5 - - + -
469E MET* 4.7 1.1 - - - -
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Residues in contact with LYS 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413E GLU* 3.4 31.1 + - - -
414E VAL* 3.9 20.4 - - + -
428E VAL* 1.3 72.6 - - - +
430E LYS* 1.3 63.0 + - - +
431E VAL* 3.5 12.2 + - + +
440E GLU* 3.3 29.4 + - - +
465E VAL 3.5 2.9 - - - +
467E ILE* 2.7 40.9 + - + +
469E MET* 3.6 24.1 - - + +
534E ASP* 2.8 45.9 + - - +
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Residues in contact with LYS 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395E GLU* 3.2 36.0 + - - +
399E TRP* 5.1 1.1 - - + -
401E THR* 5.9 1.1 - - + -
413E GLU* 3.0 40.8 + - - +
415E HIS* 4.5 17.5 - - + +
428E VAL* 4.6 8.5 - - + -
429E LYS* 1.3 70.6 - - - +
431E VAL* 1.3 61.2 + - - +
432E ARG 4.4 0.2 + - - -
464E TRP* 3.5 55.7 - - + +
465E VAL 3.8 4.3 - - - -
466E ASN* 3.3 21.3 - - - +
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Residues in contact with VAL 431 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413E GLU* 5.1 4.3 - - - +
429E LYS* 3.8 14.4 - - + +
430E LYS* 1.3 79.7 - - - +
432E ARG* 1.3 75.4 + - - +
435E VAL* 4.7 7.0 - - + +
436E PHE* 4.1 27.8 - - + +
440E GLU* 4.1 15.0 - - + +
464E TRP* 3.6 6.9 - - - -
465E VAL* 2.8 42.5 + - - +
467E ILE* 3.7 28.0 - - + -
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Residues in contact with ARG 432 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431E VAL* 1.3 78.8 - - - +
433E LEU* 1.3 64.7 + - - +
434E GLU* 3.7 28.0 + - - +
435E VAL* 3.8 25.4 - - + +
436E PHE* 3.1 22.6 + - - +
463E PRO 3.8 5.4 - - - +
464E TRP* 3.6 28.7 - - + -
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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