Contacts of the strand formed by residues 312 - 317 (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 312 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A GLY* 4.5 2.1 - - - -
273A SER* 3.0 28.6 + - - +
284A GLY* 4.0 16.4 - - - +
285A SER 3.1 10.4 + - - +
288A GLY* 3.6 31.6 - - - +
289A HIS 4.3 1.3 - - - +
290A ILE* 4.2 13.2 - - + -
308A HIS* 3.8 20.2 - - + -
310A GLN 3.3 0.2 + - - -
311A GLU* 1.3 76.4 - - - +
313A CYS* 1.3 59.0 + - - +
314A GLY 3.6 21.1 - - - +
315A LEU* 4.4 2.7 - - + -
326A SER* 4.3 11.4 - - - -
327A GLY 3.6 7.2 - - - +
328A GLY* 4.4 0.2 - - - -
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Residues in contact with CYS 313 (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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186A TYR* 3.6 49.6 - - + +
188A ASN* 3.0 26.5 + - - +
273A SER* 4.2 1.6 - - - -
311A GLU* 4.0 2.9 - - + +
312A VAL* 1.3 74.0 - - - +
314A GLY* 1.3 58.8 + - - +
327A GLY 2.9 5.3 + - - -
328A GLY 3.9 20.6 - - - -
329A ASN 3.9 3.6 - - - -
357A ALA* 4.5 3.1 - - - -
358A VAL 3.6 26.5 - - - -
359A LYS* 3.5 20.1 - - + +
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Residues in contact with GLY 314 (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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188A ASN* 5.2 0.7 - - - -
312A VAL* 3.5 4.5 - - - +
313A CYS* 1.3 80.6 - - - +
315A LEU* 1.3 61.5 + - - +
316A ARG* 5.2 2.2 - - - -
326A SER* 3.1 5.5 - - - -
327A GLY 2.7 36.4 + - - +
358A VAL 4.2 1.3 - - - -
359A LYS 3.6 17.7 - - - -
361A VAL* 4.1 10.1 - - - -
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Residues in contact with LEU 315 (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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273A SER* 3.6 22.2 - - - +
274A LEU* 3.9 6.0 - - - +
275A SER* 3.5 12.8 - - - +
282A SER* 3.6 27.4 - - - +
283A SER* 3.7 4.0 - - - -
284A GLY* 3.5 28.9 - - - +
290A ILE* 3.9 17.5 - - + -
312A VAL* 4.4 1.6 - - + -
314A GLY* 1.3 75.4 - - - +
316A ARG* 1.3 85.3 + - - +
324A LEU* 3.8 20.4 - - + -
325A ALA 3.4 13.9 - - - +
326A SER* 3.8 18.2 - - - -
361A VAL* 4.8 0.8 - - - +
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Residues in contact with ARG 316 (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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188A ASN* 4.9 12.3 + - - -
274A LEU 4.6 7.5 + - - -
275A SER* 3.5 6.7 + - - +
314A GLY* 5.2 0.6 - - - -
315A LEU* 1.3 94.5 + - - +
317A TRP* 1.3 69.9 + - - +
324A LEU* 3.4 4.0 - - - +
325A ALA 2.8 36.5 + - - -
359A LYS 4.4 8.1 + - - -
360A ALA* 5.6 0.4 - - - +
361A VAL* 2.9 52.5 + - + +
362A ALA* 4.7 4.6 - - - +
363A TRP* 2.9 22.2 + - + +
404A SER* 6.4 0.4 - - - -
405A ILE 5.8 0.8 + - - -
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Residues in contact with TRP 317 (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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275A SER* 3.0 36.9 + - - +
276A TRP 3.6 17.0 - - - +
277A ASN* 3.3 41.8 - - + +
280A ILE* 4.7 8.3 - - + +
282A SER* 2.9 19.5 + - - +
292A HIS* 3.6 29.2 - + - -
316A ARG* 1.3 80.9 - - - +
318A ALA* 1.3 67.4 + - - +
319A PRO* 3.7 2.1 - - - +
321A GLY 3.6 17.0 - - - -
323A HIS 3.3 30.7 - - - -
324A LEU* 3.4 18.1 - - + +
337A PRO 4.8 1.8 - - - -
338A SER* 4.1 25.6 - - - -
363A TRP* 3.5 6.8 - - - -
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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