Contacts of the strand formed by residues 402 - 413 (chain A) in PDB entry 1QQJ
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 402 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLU 4.1 6.5 + - - +
9A ASP* 3.7 27.4 + - - +
10A SER 3.2 20.2 + - - +
11A ASP* 2.7 31.3 + - - +
13A PRO* 3.0 29.4 - - - +
393A THR* 6.2 2.6 - - - -
394A GLY 4.7 2.2 + - - -
395A HIS* 3.5 51.9 + - + +
396A CYS 3.2 13.0 - - - +
397A GLN* 4.3 11.5 + - - +
401A TYR* 1.3 78.7 - - - +
403A VAL* 1.3 64.4 + - - +
404A GLY 3.7 0.2 - - - -
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Residues in contact with VAL 403 (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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11A ASP 4.1 1.8 - - - -
15A GLN 3.9 21.1 - - - +
16A ASN* 3.7 22.2 - - - +
264A VAL* 3.8 19.7 - - + -
268A ALA* 3.9 12.6 - - + +
269A LEU* 4.2 12.1 - - + -
272A PHE* 3.9 20.0 - - + -
395A HIS* 3.3 1.8 - - - -
396A CYS* 2.8 43.7 + - + +
401A TYR* 4.1 12.5 - - + -
402A ARG* 1.3 75.0 - - - +
404A GLY* 1.3 57.4 + - - +
405A PHE* 4.2 4.4 - - + -
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Residues in contact with GLY 404 (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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11A ASP* 2.9 38.8 + - - +
12A PHE* 4.0 4.9 - - - -
16A ASN* 3.0 18.9 + - - +
264A VAL* 3.8 6.8 - - - +
394A GLY 3.6 6.5 - - - -
395A HIS* 3.8 3.6 - - - -
402A ARG 3.7 1.2 - - - -
403A VAL* 1.3 76.2 - - - +
405A PHE* 1.3 64.6 + - - -
406A GLY 3.5 2.8 + - - -
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Residues in contact with PHE 405 (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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12A PHE* 4.9 4.3 - - - -
202A MET* 3.5 26.2 - - + -
228A MET* 3.6 22.9 - - + -
229A VAL* 4.4 7.9 - - - -
230A LEU* 3.7 22.2 - - + +
260A SER* 4.0 16.6 + - - -
261A PRO* 5.6 0.3 - - - +
262A TRP* 4.7 12.7 - - - +
264A VAL* 3.5 29.2 - - + -
269A LEU* 3.8 33.0 - - + -
297A ILE* 3.7 23.1 - - + -
394A GLY* 3.0 26.4 + - - +
396A CYS* 4.8 0.7 - - - -
403A VAL 4.2 9.0 - - - -
404A GLY* 1.3 77.0 - - - -
406A GLY* 1.3 63.5 + - - +
407A GLN 3.5 1.7 + - - -
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Residues in contact with GLY 406 (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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11A ASP* 2.9 21.1 + - - +
12A PHE* 4.2 15.2 - - - -
230A LEU* 3.8 2.0 - - - +
262A TRP* 5.3 4.7 - - - -
393A THR* 3.6 24.4 - - - +
394A GLY 4.1 1.7 + - - -
404A GLY 3.5 1.2 + - - -
405A PHE* 1.3 79.0 - - - +
407A GLN* 1.3 62.2 + - - +
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Residues in contact with GLN 407 (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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169A SER* 3.2 19.7 + - - +
170A GLY* 6.1 0.2 - - - -
230A LEU* 4.3 0.9 - - - -
260A SER* 3.2 18.5 - - - -
261A PRO* 3.8 4.8 - - - +
391A ILE* 3.9 30.0 - - + +
392A ILE 3.3 9.6 - - - +
393A THR* 4.0 7.1 - - + +
405A PHE 3.5 1.0 + - - -
406A GLY* 1.3 77.0 - - - +
408A CYS* 1.3 61.7 + - - +
409A ALA* 3.7 15.0 - - - +
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Residues in contact with CYS 408 (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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169A SER* 3.4 4.5 - - - -
230A LEU* 3.8 21.3 - - + -
231A MET* 3.9 8.1 - - - -
232A ASN* 3.6 21.3 + - - +
258A THR* 3.5 39.7 - - - -
260A SER 4.0 7.9 - - - +
390A VAL 3.8 1.6 - - - +
391A ILE* 3.7 1.1 - - - -
392A ILE* 2.9 40.2 + - + +
407A GLN* 1.3 75.5 - - - +
409A ALA* 1.3 59.0 + - - +
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Residues in contact with ALA 409 (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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169A SER* 2.8 15.8 + - - +
170A GLY* 2.7 33.0 + - - +
171A THR 4.2 0.5 + - - -
234A TRP* 4.9 1.3 - - - -
258A THR* 3.7 13.6 - - - +
389A GLU* 5.1 7.0 - - - +
390A VAL 3.4 6.1 - - - -
391A ILE* 3.9 20.0 - - + +
407A GLN* 3.7 20.2 - - - +
408A CYS* 1.3 73.6 - - - +
410A GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 410 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A GLY* 4.9 3.1 - - - -
171A THR 4.0 13.2 - - - -
173A ILE* 5.0 0.7 - - - -
234A TRP* 3.6 24.7 - - - -
258A THR* 5.3 0.4 - - - -
388A ASP 4.0 0.2 - - - +
389A GLU* 3.4 5.9 - - - +
390A VAL 2.9 32.6 + - - +
409A ALA* 1.3 77.0 - - - +
411A LYS* 1.3 61.1 + - - -
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Residues in contact with LYS 411 (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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170A GLY 5.6 0.8 + - - -
171A THR 4.4 3.2 + - - -
172A PRO* 3.5 12.4 - - + +
173A ILE* 2.9 24.7 + - - +
306A GLU* 5.0 11.1 + - - +
387A GLY* 3.3 30.7 - - - +
388A ASP 3.3 12.8 - - - +
389A GLU* 4.1 21.3 - - + +
410A GLY* 1.3 73.7 - - - -
412A VAL* 1.3 69.2 + - - +
413A LEU* 3.6 8.4 + - + +
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Residues in contact with VAL 412 (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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173A ILE* 3.3 10.1 - - + +
175A ARG* 4.4 2.7 - - + +
196A LEU* 3.5 34.5 - - + -
234A TRP* 4.3 13.0 - - + -
384A LEU* 4.3 18.4 - - + -
385A LEU 3.9 13.0 - - - +
386A ASP* 3.9 19.3 - - - +
387A GLY* 2.9 29.1 + - - -
388A ASP* 2.9 20.5 + - + +
390A VAL* 5.9 0.2 - - + -
411A LYS* 1.3 74.6 - - - +
413A LEU* 1.3 76.0 + - - +
414A PRO* 4.3 0.9 - - - +
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Residues in contact with LEU 413 (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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172A PRO* 3.7 36.6 - - + -
173A ILE 2.8 8.1 + - - +
174A ARG* 3.6 43.3 - - + +
175A ARG* 2.9 29.1 + - - +
386A ASP* 4.3 0.4 - - - -
411A LYS* 4.8 9.2 - - + +
412A VAL* 1.3 82.3 - - - +
414A PRO* 1.3 72.8 - - + +
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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