Contacts of the strand formed by residues 320 - 329 (chain A) in PDB entry 3QTC
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 ILE 320 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A LEU* 3.7 21.7 - - + +
312A LEU* 4.0 25.1 - - + +
313A ASP* 3.9 13.9 - - - +
316A LEU* 3.5 46.7 - - + +
317A PRO 3.7 6.7 - - - +
318A ASP* 4.8 2.0 - - - +
319A PRO* 1.3 72.4 - - + +
321A LYS* 1.3 61.3 + - - +
322A ILE* 4.1 13.7 - - + -
348A TRP 3.6 1.4 - - - +
349A GLN* 3.2 4.0 - - - -
350A MET* 2.8 62.0 + - + +
415A LYS* 5.6 0.7 - - - +
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Residues in contact with LYS 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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257A ARG 3.0 27.4 + - - -
258A GLY* 3.5 19.5 - - - +
259A PHE* 3.5 25.5 - - + -
260A LEU* 2.8 23.2 + - - +
316A LEU* 6.0 1.5 - - - +
319A PRO* 3.7 19.6 + - + +
320A ILE* 1.3 78.0 - - - +
322A ILE* 1.3 66.4 + - - +
348A TRP 3.5 3.8 - - - -
349A GLN* 3.6 35.3 - - + +
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Residues in contact with ILE 322 (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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259A PHE* 3.5 7.4 - - - -
260A LEU* 3.4 17.7 - - + +
262A ILE* 4.0 6.7 - - + -
305A LEU* 3.8 43.2 - - + +
308A TYR* 4.0 11.2 - - + -
309A LEU* 3.8 22.7 - - + +
312A LEU* 3.7 27.1 - - + -
316A LEU* 5.8 0.7 - - + -
320A ILE* 4.1 9.4 - - + -
321A LYS* 1.3 81.5 - - - +
323A PHE* 1.3 64.4 + - - +
347A PHE 3.7 0.2 - - - -
348A TRP* 2.9 45.4 + - + +
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Residues in contact with PHE 323 (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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250A ILE 4.7 0.2 - - - -
251A THR* 3.8 39.0 - - + -
254A PHE* 3.7 15.3 - - + -
255A VAL* 3.8 7.0 - - + -
259A PHE* 3.6 29.2 - - + -
260A LEU 3.0 13.4 + - - +
261A GLU* 3.5 37.2 - - + -
262A ILE* 2.9 30.0 + - - +
305A LEU* 5.0 2.7 - - - -
322A ILE* 1.3 78.2 - - - +
324A GLU* 1.3 65.8 + - - +
325A ILE* 4.0 14.1 - - + -
345A LEU* 4.0 17.0 - - + -
346A VAL 3.1 14.8 - - - +
347A PHE* 3.9 12.1 - - + -
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Residues in contact with GLU 324 (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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261A GLU* 6.1 0.2 - - - -
262A ILE* 3.3 22.0 - - + +
263A LYS* 3.8 3.9 - - - +
264A SER* 2.6 48.9 + - - +
298A ARG* 3.1 25.3 + - - -
301A LEU* 3.6 18.2 - - + +
304A ASN* 4.8 0.3 - - - +
305A LEU* 3.8 21.0 - - + +
323A PHE* 1.3 79.6 - - - +
325A ILE* 1.3 77.8 + - - +
326A GLY 4.6 0.2 - - - +
345A LEU* 3.3 3.1 - - - +
346A VAL 2.9 31.8 + - - +
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Residues in contact with ILE 325 (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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247A GLU* 3.6 26.6 - - + +
250A ILE* 3.6 26.7 - - + -
251A THR* 3.4 27.1 - - - +
262A ILE 4.6 1.0 + - - -
263A LYS* 3.0 27.1 + - - +
323A PHE* 4.0 10.2 - - + -
324A GLU* 1.3 87.0 - - - +
326A GLY* 1.3 63.3 + - - +
343A THR* 3.8 9.6 - - + -
344A MET 3.2 6.7 - - - +
345A LEU* 3.7 18.4 - - + -
424A LEU* 3.8 26.0 - - + -
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Residues in contact with GLY 326 (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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247A GLU* 5.4 2.2 - - - -
298A ARG* 3.5 11.6 + - - +
301A LEU* 4.5 2.1 - - - +
325A ILE* 1.3 79.3 - - - +
327A PRO* 1.3 77.7 - - - +
328A CYS* 4.2 2.9 - - - -
343A THR* 3.9 11.2 - - - -
344A MET 2.9 30.9 + - - +
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Residues in contact with PRO 327 (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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266A ILE* 3.9 24.4 - - + +
298A ARG* 2.8 40.7 + - - +
326A GLY* 1.3 83.5 - - - +
328A CYS* 1.3 56.8 + - - +
329A TYR* 3.7 27.8 - - + +
341A GLU* 5.5 1.1 - - + -
342A PHE 3.3 11.0 - - - +
343A THR* 4.4 3.1 - - + +
442A ARG* 4.3 27.6 - - - +
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Residues in contact with CYS 328 (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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298A ARG* 3.3 8.7 - - - +
299A PRO 3.9 3.4 - - - +
300A MET* 3.8 20.9 - - - -
301A LEU* 3.3 34.1 - - - -
326A GLY 3.6 1.0 + - - +
327A PRO* 1.3 73.0 - - - +
329A TYR* 1.3 68.9 + - - +
341A GLU* 3.8 0.3 - - - -
342A PHE* 2.8 58.5 + - + -
344A MET* 4.0 16.8 - - - -
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Residues in contact with TYR 329 (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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266A ILE* 3.9 17.3 - - + +
287A GLN 4.3 2.6 - - - +
288A ILE* 5.4 0.2 - - - -
289A PHE* 3.8 17.7 + + + -
297A LEU* 3.7 49.1 - - + +
298A ARG 2.8 11.5 + - - +
299A PRO* 3.2 15.8 - - - +
327A PRO* 3.7 30.5 - - + +
328A CYS* 1.3 78.8 - - - +
330A ARG* 1.3 68.8 + - - +
340A GLU 3.3 14.6 - - - -
341A GLU* 2.7 46.8 + - + +
342A PHE* 4.5 0.2 - - - -
442A ARG* 5.6 0.3 + - - -
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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