Contacts of the strand formed by residues 329 - 337 (chain B) in PDB entry 4X7C
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 LYS 329 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328B GLY* 1.3 74.6 - - - +
330B ILE* 1.3 62.4 + - - +
350B THR* 4.0 11.0 - - + -
351B VAL 3.5 4.0 - - - -
352B TYR* 3.4 40.4 - - + -
388B VAL* 3.3 6.1 - - - +
389B ILE* 3.0 56.3 + - + +
390B GLN* 5.5 0.7 - - - -
391B ASP* 4.6 12.3 - - - +
399B GLU* 2.6 41.2 + - - +
400B PRO* 5.0 2.0 - - - +
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Residues in contact with ILE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B PHE* 4.2 4.7 - - + -
284B CYS* 4.3 5.8 - - + -
324B PRO* 3.5 38.6 - - + -
326B PHE* 3.6 31.2 - - + -
328B GLY 4.7 2.0 - - - +
329B LYS* 1.3 73.9 - - - +
331B GLN* 1.3 62.0 + - - +
350B THR* 3.4 3.8 - - - -
351B VAL* 3.0 37.4 + - + +
353B THR* 4.1 11.0 - - + -
383B PHE* 3.5 25.5 - - + -
385B PRO* 4.0 17.5 - - + -
387B GLY 3.4 10.8 - - - +
388B VAL* 4.3 4.3 - - + -
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Residues in contact with GLN 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A LEU* 4.6 3.5 - - + +
346A GLY 4.9 1.2 - - - +
329B LYS 3.9 1.6 + - - -
330B ILE* 1.3 74.3 - - - +
332B GLY* 1.3 62.9 + - - +
348B LYS* 3.5 41.1 + - + +
349B ALA 3.4 11.0 - - - +
350B THR* 3.0 20.3 + - + +
383B PHE* 3.9 2.0 - - - -
385B PRO* 3.8 0.7 - - - +
386B VAL* 2.8 22.7 + - - +
387B GLY 2.7 21.0 + - - +
389B ILE* 4.0 22.7 - - + +
441B CYS* 3.2 41.3 - - + +
442B SER* 5.6 1.8 - - - -
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Residues in contact with GLY 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A LEU* 4.1 6.1 - - - +
331B GLN* 1.3 76.1 - - - +
333B LEU* 1.3 63.1 + - - +
348B LYS* 3.4 12.0 - - - +
349B ALA 2.9 30.1 + - - -
383B PHE* 3.6 7.5 - - - -
384B THR 3.1 15.5 - - - -
386B VAL* 3.9 9.4 - - - -
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A GLN* 4.1 25.8 - - + +
332A GLY* 4.7 2.9 - - - +
333A LEU* 3.9 24.2 - - + -
348A LYS* 4.1 10.8 - - + -
386A VAL* 3.7 42.6 - - + -
441A CYS* 4.2 11.0 - - + -
332B GLY* 1.3 75.3 - - - +
334B LEU* 1.3 60.1 + - - +
335B THR* 3.9 7.2 + - + +
346B GLY* 5.4 0.9 - - - -
347B HIS 3.5 10.1 - - - +
348B LYS* 3.8 23.8 - - - +
382B LYS 3.6 1.6 - - - +
383B PHE* 3.5 4.7 - - - -
384B THR* 2.9 33.0 + - - -
386B VAL* 4.8 0.8 - - - +
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Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B VAL* 5.2 2.5 - - + -
299B TYR* 5.0 7.6 - - + -
301B MET* 3.6 28.7 - - + -
332B GLY 4.3 0.2 - - - -
333B LEU* 1.3 72.8 - - - +
335B THR* 1.3 58.8 + - - +
346B GLY* 3.1 3.6 - - - -
347B HIS 2.8 39.6 + - - +
349B ALA* 3.8 21.2 - - + +
367B PHE* 4.0 21.8 - - + -
369B THR* 4.3 6.1 - - + -
375B PHE* 3.4 26.5 - - + -
381B THR* 4.0 12.3 - - + -
382B LYS 3.3 13.2 - - - +
383B PHE* 3.8 17.0 - - + -
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Residues in contact with THR 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A VAL* 3.8 28.8 - - + +
439A PRO* 3.8 18.0 - - + +
440A GLY 3.7 12.1 - - - +
441A CYS* 3.8 20.4 - - - -
333B LEU* 4.3 8.3 - - + +
334B LEU* 1.3 78.2 - - - +
336B GLN* 1.3 63.6 + - - +
345B ARG 3.3 4.0 - - - -
346B GLY* 4.4 3.6 - - - -
375B PHE* 4.4 0.7 - - - -
381B THR* 3.3 6.3 - - - +
382B LYS* 2.9 46.8 + - - +
384B THR* 5.3 0.5 + - - -
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Residues in contact with GLN 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A GLY 4.4 1.3 - - - -
290B VAL* 3.9 1.2 - - - +
335B THR* 1.3 78.9 - - - +
337B THR* 1.3 71.8 + - - +
344B THR* 3.2 8.3 - - - -
345B ARG* 2.8 61.9 + - + +
375B PHE* 3.7 24.4 - - + +
376B GLU* 2.9 47.5 + - - +
379B GLN* 3.9 11.1 + - + +
380B ASN 3.4 13.7 - - - +
381B THR* 3.1 20.6 + - - +
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Residues in contact with THR 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A PRO* 5.8 0.2 - - - +
440A GLY 4.5 4.5 + - - -
447A MET* 3.7 24.4 - - + -
336B GLN* 1.3 79.5 - - - +
338B THR* 1.3 76.5 + - - +
339B LYS* 3.6 4.6 + - - +
342B GLY* 3.9 13.9 - - - -
343B SER 3.4 8.5 - - - +
344B THR* 3.5 11.8 - - + +
379B GLN* 3.4 22.2 - - - +
380B ASN* 3.4 15.4 + - - +
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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