Contacts of the strand formed by residues 285 - 294 (chain A) in PDB entry 3QFS
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 285 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A GLN* 3.4 16.4 - - + -
279A PHE* 3.4 42.0 - + + +
283A ASN 3.7 1.0 + - - -
284A PRO* 1.3 72.7 - - - +
286A LEU* 1.3 72.8 + - - +
287A ALA* 3.2 17.8 + - + -
309A ASP 3.5 23.1 - - - -
310A ILE* 3.8 9.6 - - - -
311A SER 3.6 19.1 - - - -
312A ASP* 4.6 2.9 - - + -
313A SER* 3.5 22.4 - - - -
315A ILE* 3.9 12.1 - - + -
512A VAL 3.2 0.2 - - - +
514A MET* 2.8 36.5 + - - +
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Residues in contact with LEU 286 (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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272A TYR* 3.7 55.2 - - + +
275A GLN* 2.8 22.5 + - - +
284A PRO 3.9 7.4 - - - +
285A PHE* 1.3 83.1 - - - +
287A ALA* 1.3 63.8 + - - +
288A ALA 3.8 1.4 + - - -
511A LEU* 3.9 41.4 - - + +
512A VAL 3.6 3.8 - - - -
513A PRO* 3.8 29.2 - - + -
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Residues in contact with ALA 287 (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 PHE* 3.2 8.8 + - + -
286A LEU* 1.3 72.6 - - - +
288A ALA* 1.3 64.3 + - - +
289A VAL* 3.6 1.2 + - - +
308A LEU* 3.8 25.2 - - + +
309A ASP 3.4 19.7 - - - +
310A ILE* 4.2 3.4 - - + -
511A LEU* 3.4 2.4 - - - -
512A VAL* 2.8 41.9 + - - +
514A MET* 3.9 14.1 - - + -
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Residues in contact with ALA 288 (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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286A LEU 3.8 3.0 + - - -
287A ALA* 1.3 72.3 - - - +
289A VAL* 1.3 64.5 + - - +
290A THR* 3.3 5.9 + - + -
308A LEU* 3.6 1.1 - - - -
309A ASP* 2.8 47.9 + - + +
509A ARG* 4.4 13.7 - - + -
510A ALA 3.3 8.3 - - - +
511A LEU* 3.7 13.7 - - + -
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ALA* 1.3 70.7 - - - +
290A THR* 1.3 58.0 + - - +
291A THR 3.4 26.9 - - - +
292A ASN* 4.1 9.2 - - + -
306A LEU* 4.1 11.2 - - + -
307A GLU 3.6 6.3 - - - +
308A LEU* 3.7 9.4 - - + -
500A LYS* 3.9 17.0 - - + +
502A PRO* 3.1 33.9 - - + +
509A ARG* 5.9 0.7 - - - +
510A ALA* 2.8 28.4 + - + +
512A VAL* 3.6 31.4 - - + -
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Residues in contact with THR 290 (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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288A ALA* 3.9 6.1 - - + +
289A VAL* 1.3 76.6 - - - +
291A THR* 1.3 65.7 + - - +
307A GLU* 2.9 26.3 + - - +
309A ASP* 3.8 33.7 + - + +
471A SER* 5.0 1.9 + - - -
502A PRO* 3.9 12.6 - - - +
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Residues in contact with THR 291 (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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289A VAL* 3.4 9.8 - - - +
290A THR* 1.3 84.8 + - - +
292A ASN* 1.3 63.8 + - - +
293A ARG* 4.0 31.2 - - + +
305A HIS* 4.2 12.6 - - - +
306A LEU* 3.1 4.3 - - - -
307A GLU* 3.0 51.0 + - + -
502A PRO* 4.2 2.2 - - - -
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Residues in contact with ASN 292 (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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289A VAL* 4.1 3.4 - - + -
291A THR* 1.3 76.3 - - - +
293A ARG* 1.3 62.3 + - - +
302A HIS* 5.4 2.1 + - - -
304A MET* 4.2 12.0 - - - +
305A HIS 3.5 4.3 - - - -
306A LEU* 3.8 19.9 - - - +
497A LEU 3.0 23.0 + - - -
498A ARG* 3.4 14.4 + - - +
500A LYS 2.9 28.5 + - - +
502A PRO* 4.0 15.7 - - + +
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Residues in contact with ARG 293 (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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291A THR* 4.0 15.4 - - + +
292A ASN* 1.3 76.5 + - - +
294A LYS* 1.3 68.6 + - - +
295A LEU* 3.6 22.7 + - - +
302A HIS* 5.4 0.9 - - - -
304A MET* 3.3 5.9 - - - +
305A HIS* 2.8 72.8 + - + +
307A GLU* 5.2 1.2 + - - -
578A TYR* 4.4 3.4 - - - -
581A GLU* 2.9 30.4 + - - -
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Residues in contact with LYS 294 (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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293A ARG* 1.3 82.3 + - - +
295A LEU* 1.3 59.8 + - - +
296A ASN* 3.2 39.3 - - - +
297A GLN 4.7 1.8 + - - -
298A GLY 2.8 30.1 + - - -
299A THR* 4.0 16.6 - - - +
301A ARG 4.4 1.7 + - - -
302A HIS* 3.9 31.8 + - + +
303A LEU 3.5 6.3 - - - +
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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