Contacts of the strand formed by residues 356 - 361 (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 TYR 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306A GLU* 4.8 2.8 + - - -
328A GLY 4.4 6.9 + - - -
330A ILE* 3.5 44.4 - - + +
333A VAL* 4.1 6.9 - - - +
351A PHE* 3.8 15.7 - + - -
352A HIS* 4.1 0.2 - - - -
353A THR* 3.2 45.3 + - + +
354A TYR 3.5 4.9 - - - -
355A GLY* 1.3 83.6 - - - +
357A TYR* 1.3 67.5 + - - +
358A LEU* 3.7 27.4 - - + -
405A ARG* 5.9 1.6 - - - -
406A ALA* 4.3 4.3 - - + -
409A LEU* 4.5 19.7 - - + -
434A PHE* 4.0 16.8 - + + -
435A VAL 3.3 15.5 - - - +
437A THR* 3.4 5.4 + - - -
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Residues in contact with TYR 357 (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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350A HIS* 3.6 17.9 - - + +
351A PHE* 3.3 8.3 - - - +
352A HIS* 3.5 25.4 - - + -
353A THR 4.3 1.1 - - - -
356A TYR* 1.3 84.6 - - - +
358A LEU* 1.3 65.6 + - - +
372A LEU* 3.6 40.7 - - + +
375A ALA* 4.2 6.7 - - + -
376A SER* 3.5 28.5 - - - -
379A ALA* 3.8 5.9 - - - +
433A ALA 4.0 0.2 - - - +
434A PHE* 3.7 3.1 - - - -
435A VAL* 3.2 30.2 + - + +
437A THR* 3.5 21.7 - - + +
453A ILE* 3.2 28.8 - - + +
470A ADP 4.1 15.7 + - - -
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Residues in contact with LEU 358 (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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330A ILE* 4.3 6.3 - - + -
333A VAL* 3.7 29.4 - - + -
334A ILE* 4.1 23.8 - - + -
337A MET* 3.9 18.6 - - + -
350A HIS* 3.4 4.9 - - - -
351A PHE* 2.7 40.5 + - + +
356A TYR* 3.7 21.5 - - + -
357A TYR* 1.3 80.6 - - - +
359A ALA* 1.3 58.9 + - - +
372A LEU* 4.3 2.2 - - - -
413A LEU* 5.0 0.9 - - + -
432A LEU* 4.4 13.7 - - + -
433A ALA 3.4 11.9 - - - +
434A PHE* 4.0 24.0 - - + -
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Residues in contact with ALA 359 (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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337A MET* 4.1 1.6 - - - -
348A ARG* 5.4 2.9 - - - +
349A ILE 3.1 9.2 - - - +
350A HIS* 4.6 4.0 - - + -
358A LEU* 1.3 76.6 - - - +
360A LEU* 1.3 61.3 + - - +
361A THR* 3.9 6.2 + - + +
368A VAL* 3.7 26.9 - - + +
372A LEU* 3.8 21.5 - - + -
431A GLN 3.7 1.2 - - - +
432A LEU* 3.6 5.8 - - - +
433A ALA* 3.1 31.1 + - + +
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Residues in contact with LEU 360 (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* 5.1 0.9 - - + +
337A MET* 3.5 48.5 - - + +
338A ASN* 3.4 28.3 - - - +
341A MET* 3.6 19.8 - - + +
348A ARG* 3.3 2.9 - - - -
349A ILE* 2.9 34.1 + - + +
359A ALA* 1.3 71.9 - - - +
361A THR* 1.3 61.4 + - - +
427A MET* 4.4 4.7 - - + -
430A ARG* 3.4 26.9 - - - +
431A GLN 3.4 15.3 - - - +
432A LEU* 4.2 16.4 - - + -
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Residues in contact with THR 361 (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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341A MET* 4.7 1.6 - - - -
347A GLU 3.5 3.8 - - - -
348A ARG* 3.5 25.1 - - + -
359A ALA* 3.9 1.6 + - + -
360A LEU* 1.3 83.5 - - - +
362A GLN* 1.3 62.3 + - - +
363A TYR* 2.8 42.5 + - + +
368A VAL* 4.0 30.0 - - + +
430A ARG* 3.1 6.8 - - - +
431A GLN* 2.8 41.0 + - - +
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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