Contacts of the strand formed by residues 431 - 436 (chain A) in PDB entry 1GC5
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 431 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359A ALA 3.7 0.7 - - - +
360A LEU* 3.4 9.7 - - - +
361A THR* 2.8 33.3 + - - +
363A TYR 3.7 13.4 + - - +
364A ARG* 3.3 17.5 - - + +
365A GLY 2.9 43.2 + - - +
368A VAL* 4.0 14.6 - - - +
420A PHE* 3.4 26.1 - - + -
424A LEU* 3.6 13.7 - - - +
425A ILE 3.4 15.5 - - - +
426A ASP* 4.6 1.0 + - - +
427A MET* 5.2 0.9 - - - -
430A ARG* 1.3 75.8 - - - +
432A LEU* 1.3 69.7 + - - +
433A ALA* 4.7 1.6 - - - +
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Residues in contact with LEU 432 (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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334A ILE* 3.6 42.8 - - + -
337A MET* 4.7 3.8 - - + -
358A LEU* 4.4 17.3 - - + -
359A ALA 3.6 17.5 - - - +
360A LEU* 4.2 19.3 - - + -
413A LEU* 5.6 1.6 - - + -
417A PHE* 4.8 3.1 - - + -
423A GLY 3.7 0.2 - - - +
424A LEU* 3.6 2.3 - - - -
425A ILE* 2.8 66.1 + - + +
427A MET* 4.4 12.8 - - + +
431A GLN* 1.3 78.5 - - - +
433A ALA* 1.3 67.9 + - - +
434A PHE* 5.7 0.2 - - + -
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Residues in contact with ALA 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A LEU* 3.4 8.7 - - - +
359A ALA 3.1 35.1 + - - +
368A VAL* 4.3 21.3 - - + -
369A ARG* 4.4 8.3 - - - +
372A LEU* 4.0 12.0 - - + +
423A GLY 2.9 9.9 - - - +
424A LEU* 3.9 15.5 - - + -
431A GLN* 4.7 1.3 - - - +
432A LEU* 1.3 77.4 - - - +
434A PHE* 1.3 61.8 + - - +
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Residues in contact with PHE 434 (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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12A TRP* 3.6 2.5 - + - -
330A ILE* 4.2 10.8 - - + -
356A TYR* 4.0 21.1 - + + -
357A TYR 3.7 6.3 - - - -
358A LEU* 4.0 17.9 - - + -
369A ARG* 4.2 0.7 - - - +
372A LEU* 5.0 0.2 - - - -
406A ALA* 3.1 37.2 - - + -
407A ILE* 5.4 0.2 - - - -
409A LEU* 4.8 6.1 - - + -
410A GLU* 3.9 32.3 - - + -
413A LEU* 3.4 30.7 - - + -
423A GLY* 2.7 33.2 + - - +
425A ILE* 5.2 4.0 - - + -
432A LEU* 4.3 0.6 - - + -
433A ALA* 1.3 74.6 - - - +
435A VAL* 1.3 71.2 + - - +
436A PRO* 3.7 23.8 - - + -
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Residues in contact with VAL 435 (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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12A TRP* 4.1 3.6 - - + -
16A TYR* 4.3 2.2 - - - +
356A TYR* 3.3 4.9 - - - +
357A TYR* 3.2 31.7 + - + +
369A ARG* 3.8 23.8 - - + +
372A LEU* 4.0 28.9 - - + +
373A LEU* 3.6 35.0 - - + -
376A SER* 4.6 0.2 - - - -
434A PHE* 1.3 86.5 - - - +
436A PRO* 1.3 75.8 - - - +
437A THR* 4.2 10.1 - - + -
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Residues in contact with PRO 436 (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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12A TRP* 3.4 53.6 - - + +
16A TYR* 2.6 27.2 + - - -
355A GLY 3.8 0.2 - - - +
402A THR* 3.6 21.3 - - + +
403A ASN 4.2 2.0 - - - +
406A ALA* 3.6 35.2 - - + -
407A ILE* 4.2 3.4 - - + -
434A PHE* 3.7 7.8 - - + -
435A VAL* 1.3 83.2 - - - +
437A THR* 1.3 54.5 + - - +
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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