Contacts of the strand formed by residues 313 - 320 (chain A) in PDB entry 5A19
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 ARG 313 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A TYR* 2.9 25.8 + - + +
142A ALA 3.3 9.6 - - - +
143A THR* 4.2 6.3 - - - +
193A GLY* 3.0 25.7 + - - -
194A ALA* 4.4 7.6 - - + +
195A VAL* 3.8 18.1 - - - +
274A TRP* 3.6 18.8 - - - -
275A GLY 5.7 1.0 - - - +
306A VAL* 4.1 0.9 - - - +
311A CYS* 3.6 2.5 - - - +
312A ARG* 1.3 79.9 - - + +
314A VAL* 1.3 67.4 + - - +
334A HIS* 3.1 24.1 - - - +
335A TYR* 3.3 42.9 + - + -
337A THR* 3.1 16.1 + - + -
408A PEG 3.1 44.5 + - - -
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Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLY 3.9 0.2 - - - +
141A TYR* 3.3 10.8 - - - -
142A ALA 3.0 26.9 + - - +
302A ALA* 3.4 38.4 - - + +
305A LEU* 4.0 12.8 - - + -
306A VAL* 3.9 10.1 - - + -
311A CYS* 3.6 15.3 - - - -
313A ARG* 1.3 78.9 - - - +
315A LEU* 1.3 66.0 + - - +
316A VAL* 4.6 1.3 - - + -
332A ILE* 3.7 26.5 - - + -
333A PHE 3.4 13.5 - - - +
334A HIS* 4.4 2.0 - - + -
335A TYR* 4.1 2.4 - - - -
345A LEU* 5.1 0.2 - - + -
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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
----------------------------------------------------------
139A PHE* 3.9 30.3 - - + -
140A GLY 3.4 15.3 - - - +
141A TYR* 4.3 3.4 - - + -
275A GLY* 3.7 11.7 - - - +
276A ALA* 3.7 32.3 - - + +
314A VAL* 1.3 74.8 - - - +
316A VAL* 1.3 61.4 + - - +
332A ILE* 3.5 3.8 - - - -
333A PHE* 2.8 62.1 + - + +
335A TYR* 3.7 22.2 - - + +
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Residues in contact with VAL 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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138A MET 3.8 0.2 - - - +
139A PHE* 3.1 10.0 - - - +
140A GLY 2.8 37.4 + - - +
298A ALA* 4.1 20.4 - - + +
301A VAL* 4.1 20.9 - - + -
302A ALA* 4.0 24.0 - - + -
305A LEU* 4.7 0.9 - - + -
314A VAL* 4.6 7.0 - - + -
315A LEU* 1.3 78.2 - - - +
317A GLN* 1.3 67.5 + - - +
318A VAL* 4.7 6.5 - - + -
330A ILE* 4.8 4.3 - - + -
331A SER 3.3 9.0 - - - +
332A ILE* 3.8 23.1 - - + -
349A VAL* 5.8 0.2 - - + -
355A LEU* 5.8 1.8 - - + -
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Residues in contact with GLN 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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137A LEU* 3.5 22.8 - - - +
138A MET 3.3 9.2 - - - +
139A PHE* 3.2 39.8 - - + -
315A LEU 4.3 0.2 - - - -
316A VAL* 1.3 74.3 - - - +
318A VAL* 1.3 79.7 + - - +
319A SER* 5.6 1.1 - - - -
329A SER* 4.4 10.6 + - - -
330A ILE* 3.4 3.7 - - - +
331A SER* 2.9 50.8 + - - +
333A PHE* 4.7 5.9 - - + -
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Residues in contact with VAL 318 (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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137A LEU* 3.3 5.4 - - - +
138A MET* 2.8 51.9 + - + +
294A ALA* 4.1 14.6 - - + +
298A ALA* 4.7 5.6 - - + -
316A VAL* 4.7 6.7 - - + -
317A GLN* 1.3 83.1 - - - +
319A SER* 1.3 61.1 + - - +
320A TYR* 3.9 26.2 - - + +
327A PRO* 4.7 1.8 - - + -
329A SER* 3.4 7.4 - - - +
330A ILE* 4.1 15.3 - - + -
355A LEU* 3.7 30.5 - - + -
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Residues in contact with SER 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLY 3.2 13.2 - - - -
137A LEU* 4.2 9.4 - - - -
317A GLN* 5.6 2.0 - - - -
318A VAL* 1.3 77.2 - - - +
320A TYR* 1.3 64.0 + - - +
327A PRO* 3.1 9.7 - - - +
328A LEU* 2.7 37.3 + - - +
329A SER* 2.5 35.1 + - - -
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Residues in contact with TYR 320 (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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132A ALA* 3.9 24.0 - - + -
134A ASP 4.0 6.3 - - - +
135A GLN* 3.3 5.0 - - - +
136A GLY 2.9 25.3 + - - +
138A MET* 3.7 14.6 - - - -
290A VAL* 3.8 18.4 - - + -
294A ALA* 3.4 33.5 - - + +
318A VAL* 3.9 17.1 - - + +
319A SER* 1.3 77.3 - - - +
321A ALA* 1.3 60.1 + - - +
324A VAL 4.7 0.9 - - - -
325A SER 3.9 13.9 - - - -
326A HIS 4.4 1.8 - - - -
327A PRO* 3.9 27.6 - - + +
328A LEU* 3.8 14.2 - - - +
355A LEU* 2.6 39.9 + - - +
357A PRO* 4.4 1.8 - - + -
360A ILE* 4.2 1.4 - - - +
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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