Contacts of the strand formed by residues 357 - 362 (chain A) in PDB entry 3GVU
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 PHE 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A LYS 3.7 0.2 - - - +
318A THR* 3.2 28.4 + - - -
319A LEU* 3.2 27.1 + - + +
320A LYS 6.0 0.2 - - - -
326A VAL* 3.9 31.0 - - + -
329A PHE* 3.4 24.8 - + + -
330A LEU* 4.7 12.1 - - + -
351A CYS 3.1 15.3 - - - +
352A THR* 3.6 20.0 - - + -
353A LEU 4.1 0.9 - - - -
354A GLU* 3.2 37.9 - - - -
355A PRO* 3.9 21.1 - - + -
356A PRO* 1.3 73.2 - - - +
358A TYR* 1.3 60.8 + - - +
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Residues in contact with TYR 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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285A ARG* 3.6 45.7 + - + +
288A ILE* 4.5 8.0 + - + -
290A MET* 3.5 37.0 - - + +
316A VAL* 3.5 23.3 - - + -
317A LYS 3.2 3.4 - - - -
318A THR* 3.9 14.8 - - - -
329A PHE* 3.9 2.3 - - - -
350A VAL* 3.4 6.2 - - - +
351A CYS* 2.9 55.0 + - + +
352A THR* 4.7 0.7 - - - +
356A PRO* 3.9 8.7 - - + +
357A PHE* 1.3 82.2 - - - +
359A ILE* 1.3 66.9 + - - +
360A VAL* 4.2 12.1 - - + -
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Residues in contact with ILE 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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316A VAL* 3.4 2.1 - - - -
317A LYS* 2.9 35.2 + - + +
329A PHE* 3.7 30.3 - - + +
332A GLU* 4.0 22.7 - - + +
333A ALA* 3.9 35.9 - - + +
336A MET* 3.9 6.5 - - + -
347A LEU* 3.5 26.0 - - + -
349A GLY 3.8 3.4 - - - -
350A VAL* 4.3 1.8 - - + -
358A TYR* 1.3 78.3 - - - +
360A VAL* 1.3 62.3 + - - +
361A THR* 4.5 1.1 - - + -
1001A STI 3.7 29.4 - - + +
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Residues in contact with VAL 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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283A MET* 3.9 19.5 - - + -
288A ILE* 4.4 11.2 - - + -
307A TRP* 5.2 1.3 - - + -
314A VAL* 3.7 37.9 - - + -
315A ALA 3.4 3.6 - - - +
316A VAL* 4.0 19.1 - - + -
347A LEU* 3.6 5.0 - - - +
348A LEU* 2.7 38.7 + - + -
349A GLY 2.9 25.5 + - - +
350A VAL 5.2 0.2 - - - +
358A TYR* 4.2 16.4 - - + -
359A ILE* 1.3 75.3 - - - +
361A THR* 1.3 57.8 + - - +
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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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314A VAL* 3.4 8.3 - - - +
315A ALA* 2.8 25.9 + - - +
336A MET* 3.8 18.6 - - + -
345A VAL* 3.8 10.9 - - + +
346A GLN 3.2 14.4 - - - +
347A LEU* 4.3 0.7 - - - -
348A LEU* 3.5 7.2 - - - +
359A ILE* 4.5 0.9 - - + -
360A VAL* 1.3 78.1 - - - +
362A GLU* 1.3 75.6 + - - +
1001A STI 3.0 56.1 + - + +
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Residues in contact with GLU 362 (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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312A LEU* 6.1 1.1 - - + -
313A THR 5.0 1.3 - - - -
314A VAL* 4.8 0.7 - - - +
315A ALA* 3.8 4.9 - - - +
345A VAL* 3.8 10.6 - - + +
346A GLN* 3.0 48.0 + - - +
348A LEU* 3.4 14.9 - - + +
361A THR* 1.3 91.5 + - - +
363A TYR* 1.3 61.8 + - - +
364A MET* 3.7 22.6 + - - +
424A LYS* 2.5 38.3 + - - +
1001A STI 4.4 2.6 - - - -
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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