Contacts of the strand formed by residues 403 - 409 (chain A) in PDB entry 1WCP
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 GLN 403 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A ASP* 2.9 28.5 + - - +
300A SER* 3.3 19.7 + - - +
301A TYR* 3.6 18.0 - - - +
302A VAL* 3.6 15.6 - - + +
306A ASN* 3.2 27.4 + - - +
399A LEU* 3.4 11.9 - - - +
400A GLN 3.1 21.2 + - - +
401A SER 4.3 2.9 - - - +
402A GLY* 1.3 79.5 - - - +
404A PRO* 1.3 72.3 - - + +
405A LYS* 3.3 29.4 + - + +
445A SER* 5.9 0.2 - - - -
447A LEU* 6.1 0.3 - - - +
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Residues in contact with PRO 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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297A ASP* 3.1 28.2 - - - +
299A PRO* 3.6 39.5 - - + -
300A SER* 4.4 5.4 - - - +
372A ALA* 6.5 0.9 - - + -
373A GLU* 5.5 5.2 - - + -
376A LEU* 5.4 4.9 - - + -
397A THR* 4.2 15.9 - - + -
398A GLY 3.6 12.8 - - - +
399A LEU* 4.0 9.6 - - + -
402A GLY 4.9 0.2 - - - -
403A GLN* 1.3 83.7 - - + +
405A LYS* 1.3 60.9 + - - +
406A HIS* 3.9 5.7 - - + -
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Residues in contact with LYS 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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295A LEU 5.3 4.4 + - - -
297A ASP* 2.8 29.8 + - - +
306A ASN* 3.4 30.1 + - - +
397A THR* 3.4 21.1 - - - +
398A GLY 3.4 10.0 + - - +
403A GLN* 3.3 32.6 + - - +
404A PRO* 1.3 71.8 - - - +
406A HIS* 1.3 73.5 + - - +
407A LEU* 5.0 4.0 - - + -
442A SER* 4.5 21.3 - - - +
443A ALA* 4.3 13.0 - - - +
447A LEU* 4.4 23.3 - - + -
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Residues in contact with HIS 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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294A GLU* 4.3 1.0 - - - +
295A LEU* 3.4 33.5 + - + +
296A PHE 3.5 15.7 - - - +
297A ASP* 3.5 23.7 - - + +
298A ASP* 4.5 3.2 + - - +
299A PRO* 5.0 4.4 - - + +
385A ARG* 4.2 17.8 + - - -
395A VAL* 3.9 13.7 - - + -
396A LEU 3.5 6.3 - - - -
397A THR* 3.5 24.9 + - + -
404A PRO* 3.9 22.0 - - + -
405A LYS* 1.3 94.1 + - - +
407A LEU* 1.3 70.9 - - - +
442A SER* 5.3 1.4 - - - -
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Residues in contact with LEU 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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292A GLY* 4.1 11.2 - - - -
293A ARG* 3.1 27.8 - - - +
294A GLU* 4.3 4.9 - - + -
295A LEU* 5.1 0.7 - - - +
395A VAL* 3.1 7.1 - - - -
396A LEU* 2.8 57.4 + - + +
398A GLY 5.7 0.4 - - - +
405A LYS* 5.0 1.8 - - + +
406A HIS* 1.3 86.9 - - - +
408A LEU* 1.3 57.5 + - - +
409A LEU* 4.6 0.6 - - + +
433A HIS* 5.3 3.8 - - + -
440A ILE* 5.7 2.9 - - + -
442A SER* 3.9 28.3 - - - +
447A LEU* 3.8 26.9 - - + -
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Residues in contact with LEU 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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259A GLN* 5.6 7.2 - - - +
261A PRO 5.8 0.9 - - - +
262A SER* 4.8 9.4 - - - +
292A GLY* 3.7 0.9 - - - -
293A ARG* 2.9 53.8 + - + +
295A LEU* 4.0 30.6 - - + +
393A GLN* 3.7 36.1 - - + +
394A TYR 3.8 1.8 - - - -
395A VAL* 3.9 12.1 - - + +
407A LEU* 1.3 71.4 - - - +
409A LEU* 1.3 74.2 + - - +
410A VAL* 4.1 19.1 - - + -
417A ARG 5.0 0.7 - - - +
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Residues in contact with LEU 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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291A PRO* 3.7 20.0 - - + -
292A GLY* 3.6 26.2 - - - +
293A ARG* 5.9 0.2 - - - -
384A VAL* 5.0 7.6 - - + -
393A GLN* 3.8 1.7 - - - +
394A TYR* 2.8 51.4 + - + +
396A LEU* 4.4 10.5 - - + +
407A LEU 4.6 3.8 - - - +
408A LEU* 1.3 81.7 - - - +
410A VAL* 1.3 71.2 + - - +
416A VAL* 4.0 21.5 - - + -
417A ARG 4.3 4.9 - - - +
426A VAL* 5.1 7.0 - - + -
429A LEU* 3.6 25.4 - - + -
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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