Contacts of the strand formed by residues 358 - 363 (chain A) in PDB entry 4GGA
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 VAL 358 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313A CYS* 3.6 3.3 - - - -
314A GLY* 4.0 1.0 + - - -
327A GLY* 3.2 38.0 - - - +
328A GLY 3.2 7.6 + - - +
332A LEU 4.1 13.9 - - - +
333A VAL* 3.8 24.7 - - + -
354A HIS* 3.8 26.5 - - + -
356A GLY 3.7 10.3 - - - +
357A ALA* 1.3 76.0 - - - +
359A LYS* 1.3 57.5 + - - +
360A ALA 3.6 20.6 - - - +
361A VAL* 4.3 2.7 - - + -
373A THR* 3.8 9.4 - - - -
374A GLY 3.5 10.1 - - - +
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Residues in contact with LYS 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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184A ASP 4.7 0.8 + - - -
185A TYR* 2.8 50.7 + - + +
186A TYR* 4.4 1.6 - - - -
187A LEU 2.7 29.6 + - - -
188A ASN* 3.6 17.5 - - - +
313A CYS* 3.5 25.9 - - + +
314A GLY* 3.6 13.7 - - - -
316A ARG* 4.4 6.6 + - - -
357A ALA 3.8 3.2 + - - -
358A VAL* 1.3 75.7 - - - +
360A ALA* 1.3 63.3 + - - +
361A VAL* 3.5 4.6 + - - +
374A GLY 3.7 2.4 + - - -
403A CYS* 3.4 20.0 - - + +
404A SER* 6.1 0.2 - - - -
447A LEU* 2.7 33.6 + - - +
448A SER* 3.9 3.0 + - - +
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Residues in contact with ALA 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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316A ARG* 5.6 0.2 - - - +
358A VAL* 3.6 1.9 - - - +
359A LYS* 1.3 77.8 - - - +
361A VAL* 1.3 63.3 + - - +
372A ALA 4.4 0.4 - - - -
373A THR* 3.1 8.1 - - - -
374A GLY* 2.9 39.1 + - - +
402A VAL* 3.6 20.8 + - + +
403A CYS 3.9 4.0 - - - -
404A SER* 3.7 29.4 - - - +
405A ILE* 3.9 8.3 - - + -
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Residues in contact with VAL 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 GLY* 4.1 15.3 - - - -
316A ARG* 2.9 51.5 + - + +
325A ALA* 3.7 33.0 - - + +
326A SER 4.7 0.7 - - - -
327A GLY* 4.3 13.2 - - - +
333A VAL* 6.0 0.4 - - + -
358A VAL* 4.3 9.6 - - + -
359A LYS 3.5 12.3 + - - +
360A ALA* 1.3 80.6 - - - +
362A ALA* 1.3 66.3 + - - +
371A LEU* 4.1 7.2 - - + -
372A ALA 3.5 5.4 - - - +
373A THR* 4.4 6.5 - - + -
405A ILE* 4.7 4.5 - - - +
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Residues in contact with ALA 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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316A ARG* 4.7 6.1 - - - +
361A VAL* 1.3 78.9 - - - +
363A TRP* 1.3 59.0 + - - +
371A LEU* 3.9 4.2 - - - +
372A ALA 2.8 38.2 + - - -
405A ILE* 3.4 31.6 - - + +
406A LEU* 4.6 2.2 - - + -
407A TRP* 2.9 26.0 + - + +
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Residues in contact with TRP 363 (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 ARG* 2.9 33.1 + - + +
317A TRP 3.5 8.5 - - - -
318A ALA* 3.4 26.7 - - + +
319A PRO* 3.5 21.1 - - + +
323A HIS* 3.5 33.4 - + + -
324A LEU 4.2 0.9 - - - -
325A ALA* 3.6 27.0 - - + +
335A VAL* 4.1 5.8 - - + -
362A ALA* 1.3 74.5 - - - +
364A CYS* 1.3 65.7 + - - +
365A PRO* 3.2 7.4 - - - +
368A SER 3.7 20.4 - - - +
369A ASN 4.5 0.4 - - - -
370A VAL 3.5 19.7 - - - -
371A LEU* 3.8 11.7 - - + -
387A VAL* 3.8 35.9 - - + -
407A TRP* 3.1 13.0 - - - -
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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