Contacts of the strand formed by residues 314 - 322 (chain A) in PDB entry 1JQP
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 314 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A GLU* 3.0 29.1 + - - +
285A TYR* 3.7 5.5 + - - -
289A PHE* 2.7 25.9 + - - +
290A GLY 3.0 19.9 + - - -
291A VAL 3.3 6.1 - - - +
292A VAL* 3.2 24.5 - - + +
308A PRO* 5.4 8.3 - - - +
312A CYS* 3.5 15.0 + - - +
313A LEU* 1.3 87.7 - - - +
315A TYR* 1.3 65.1 + - - +
316A TYR* 3.7 31.3 - - + +
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Residues in contact with TYR 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 6.0 2.2 - - + -
246A ILE* 3.9 28.7 - - + -
254A GLN* 4.6 2.0 + - - -
256A PRO* 3.8 19.5 - - + +
258A LEU* 4.2 13.2 - - + -
286A ALA* 3.7 1.8 - - - +
290A GLY* 2.9 5.5 - - - -
291A VAL* 2.8 51.8 + - + +
292A VAL* 5.0 0.2 - - - -
293A GLU* 3.0 36.8 + - + -
313A LEU* 3.7 29.5 - - + +
314A ARG* 1.3 76.7 - - - +
316A TYR* 1.3 65.2 + - - +
434A PRO* 6.4 0.7 - - + -
435A ILE 3.9 14.6 - - - +
437A LYS* 3.9 32.0 - - + +
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Residues in contact with TYR 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 3.6 21.3 + - - -
242A LEU* 6.1 1.3 - - - -
286A ALA* 3.1 21.8 - - - -
287A GLN 3.2 17.5 - - - +
288A ASP 3.9 6.5 - - - -
289A PHE 3.5 30.7 + - - -
290A GLY* 3.8 1.1 - - - -
314A ARG* 3.7 34.4 - - + +
315A TYR* 1.3 77.0 - - - +
317A SER* 1.3 58.4 + - - +
434A PRO* 3.6 2.8 - - - +
435A ILE* 2.8 54.1 + - + +
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Residues in contact with SER 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 3.6 16.6 - - - +
282A ALA 2.8 27.0 + - - -
283A GLY* 4.0 7.9 - - - -
286A ALA* 3.3 18.0 + - - +
287A GLN* 3.2 25.3 + - - +
316A TYR* 1.3 76.2 + - - +
318A SER* 1.3 64.4 + - - +
319A GLU 4.1 11.9 - - - -
320A TYR* 4.9 0.2 - - - -
432A ALA* 3.9 1.5 - - - +
433A ILE 3.2 11.4 + - - -
435A ILE* 4.3 2.0 - - - -
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Residues in contact with SER 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLN* 3.2 13.3 + - - +
317A SER* 1.3 73.0 - - - +
319A GLU* 1.3 66.7 + - - +
433A ILE* 2.9 27.9 + - - +
435A ILE* 3.7 27.1 - - - +
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Residues in contact with GLU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LYS* 4.7 9.7 + - - -
287A GLN* 4.4 0.8 + - - +
317A SER* 3.3 2.7 - - - -
318A SER* 1.3 88.8 + - - +
320A TYR* 1.3 98.1 + - - +
321A TYR* 3.6 24.1 - - + -
432A ALA* 3.2 3.6 - - - +
433A ILE* 2.7 41.8 + - + +
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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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59A TYR* 5.7 0.2 + - - -
69A GLU* 2.9 37.0 + - - -
76A LYS* 3.2 23.8 + - - +
279A TYR* 3.8 25.8 + + - -
283A GLY* 3.3 40.6 - - - -
284A LYS* 3.7 19.8 + - - +
287A GLN* 3.3 34.6 + - + -
288A ASP* 5.2 0.3 + - - -
317A SER* 4.9 1.6 - - - -
319A GLU* 1.3 94.6 + - - +
321A TYR* 1.3 68.6 + - - +
430A MET* 3.6 9.6 - - + -
431A ALA 3.1 8.3 - - - +
432A ALA* 3.9 1.6 - - + -
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Residues in contact with TYR 321 (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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59A TYR* 5.4 4.0 - - + +
245A ARG* 4.5 2.8 + - - -
279A TYR* 4.1 13.9 - - - -
319A GLU* 3.6 26.2 - - + -
320A TYR* 1.3 80.7 - - - +
322A TYR* 1.3 75.7 + - - +
323A VAL* 4.7 4.7 - - - -
325A GLY* 5.1 9.4 - - - +
338A GLU* 2.9 38.1 + - + -
342A HIS* 4.0 8.0 + - - -
430A MET* 3.6 3.6 - - - +
431A ALA* 2.9 48.1 + - + +
433A ILE* 4.5 13.4 - - + +
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Residues in contact with TYR 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 5.4 0.6 + - - -
61A THR* 3.6 8.5 - - + -
62A LEU 3.5 19.7 - - - -
63A ILE* 3.6 20.8 - - - +
277A PHE* 5.3 3.3 - - - +
279A TYR* 3.3 43.5 - + + +
321A TYR* 1.3 81.7 - - - +
323A VAL* 1.3 56.7 + - - +
324A GLY 3.0 0.2 + - - -
325A GLY* 2.7 32.6 + - - -
326A PHE* 3.6 21.3 - - - +
327A TYR* 3.4 21.3 - - + -
428A ILE* 3.4 39.0 - - + +
429A ALA 3.6 14.8 - - - +
430A MET* 3.8 18.6 - - + -
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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