Contacts of the strand formed by residues 314 - 321 (chain B) in PDB entry 6XPD
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 314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B PHE* 3.7 22.2 - - + -
305B ILE* 3.2 27.4 - - - +
306B TRP* 3.3 62.2 + - + +
308B LEU* 3.4 24.7 - - + -
312B GLN 3.7 3.8 + - - +
313B VAL* 1.3 79.9 - - - +
315B LEU* 1.3 74.8 + - - +
316B SER* 4.6 0.4 - - - +
344B MET* 4.4 0.2 - - - -
345B HIS* 4.4 14.4 - - - +
346B SER* 3.8 24.7 - - - +
348B THR* 6.3 1.1 - - + -
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Residues in contact with LEU 315 (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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287B VAL* 4.0 26.0 - - + -
291B ILE* 4.7 1.8 - - + -
303B LEU* 4.6 7.9 - - + -
304B HIS 3.6 6.7 - - - +
305B ILE* 4.1 23.8 - - + -
306B TRP* 5.0 0.2 - - - -
314B ILE* 1.3 80.8 - - - +
316B SER* 1.3 92.5 + - - +
317B ALA* 4.2 13.5 - - + -
338B LEU* 4.1 26.2 - - + -
342B PHE* 4.5 4.9 - - + -
344B MET* 3.6 19.5 - - + -
346B SER 3.3 5.0 + - - +
347B LEU* 3.4 27.9 - - + -
348B THR* 3.4 2.1 + - - +
349B ILE* 5.1 4.9 - - + -
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Residues in contact with SER 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A TRP* 6.0 0.2 - - - -
316A SER* 4.8 4.1 + - - -
348A THR* 4.1 15.8 + - - +
302B SER 3.3 3.5 - - - +
304B HIS* 2.9 39.2 + - - +
306B TRP* 3.5 25.9 - - - -
314B ILE* 4.6 1.0 - - - +
315B LEU* 1.3 82.8 + - - +
317B ALA* 1.3 61.0 + - - +
348B THR* 3.6 24.3 + - - +
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A THR* 4.9 0.2 - - - +
291B ILE* 4.8 3.8 - - + -
300B VAL* 4.4 5.4 - - + -
302B SER 3.6 5.4 - - - -
303B LEU* 4.2 21.3 - - + -
315B LEU* 4.2 16.0 - - + +
316B SER* 1.3 76.1 - - - +
318B HIS* 1.3 73.4 + - - +
319B VAL* 4.7 4.3 - - + -
348B THR 3.5 7.5 + - - +
349B ILE* 3.2 15.6 - - + +
350B GLN 2.9 23.9 + - - -
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Residues in contact with HIS 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A CYS* 3.5 11.4 - - + -
54A HIS* 4.3 6.7 - + - -
346A SER* 6.0 1.4 - - - -
347A LEU 3.3 16.8 + - - -
348A THR* 3.8 12.4 - - + +
300B VAL* 3.4 9.4 - - - +
301B HIS* 3.0 46.5 + + + +
302B SER* 3.9 15.5 + - - -
317B ALA* 1.3 79.2 - - - +
319B VAL* 1.3 61.7 + - - +
350B GLN* 2.7 32.2 + - + -
352B GLU* 2.3 15.4 + - + +
401B ZN 1.9 33.5 - - - -
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Residues in contact with VAL 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ILE* 4.9 8.1 - - + -
297B VAL* 4.7 17.0 - - + -
299B SER 3.6 5.8 - - - -
300B VAL* 3.6 23.3 - - + -
301B HIS* 5.5 1.3 - - - -
317B ALA* 4.1 5.4 + - + -
318B HIS* 1.3 80.1 - - - +
320B ALA* 1.3 63.2 + - - +
321B THR 4.8 0.2 - - - +
334B ILE* 5.5 4.9 - - + -
349B ILE* 3.8 17.3 - - + -
351B MET* 3.3 44.8 - - + +
352B GLU* 2.7 33.1 + - - +
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Residues in contact with ALA 320 (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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297B VAL* 4.0 0.6 - - - -
298B LEU* 2.7 39.4 + - + +
299B SER* 2.8 31.3 + - - +
301B HIS* 5.5 1.3 - - - +
319B VAL* 1.3 74.0 - - - +
321B THR* 1.3 55.1 + - - +
352B GLU* 4.2 1.8 - - + -
353B SER 3.5 24.0 - - - +
354B PRO* 4.8 6.1 - - + +
356B ASP* 4.0 12.8 - - - +
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Residues in contact with THR 321 (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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296B GLY* 2.7 31.3 + - - -
297B VAL* 4.1 3.8 - - - +
298B LEU* 3.5 13.2 - - - +
319B VAL* 4.1 2.6 - - - -
320B ALA* 1.3 74.7 - - - +
322B ALA* 1.3 76.0 + - - +
323B ALA* 3.1 4.9 + - - -
325B ARG* 4.3 1.0 - - - +
327B SER* 4.4 11.9 - - - +
330B VAL* 3.8 17.6 - - + +
351B MET* 3.7 29.4 - - + -
352B GLU 4.1 10.8 + - - +
353B SER* 5.9 0.4 - - - -
354B PRO* 3.8 12.8 - - - +
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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