Contacts of the strand formed by residues 327 - 332 (chain A) in PDB entry 5KZX
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 ALA 327 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A PHE* 3.7 25.6 - - + -
236A VAL* 5.2 0.7 - - + -
250A THR 3.2 14.8 - - - +
251A SER* 4.1 4.3 - - - -
252A LEU* 3.8 11.7 - - - +
322A LEU* 3.5 4.0 - - - +
323A GLN* 3.0 37.6 + - + +
325A SER* 3.2 13.0 + - - +
326A PRO* 1.3 77.3 - - - +
328A LEU* 1.3 61.7 + - - +
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Residues in contact with LEU 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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90A PHE* 5.2 0.4 - - - -
249A SER* 3.1 4.2 - - - -
250A THR* 2.8 40.3 + - + +
252A LEU* 4.0 12.3 - - + -
257A ILE* 3.7 10.5 - - + -
260A LEU* 4.7 1.3 - - + -
298A TYR* 3.5 33.2 - - + -
320A VAL* 3.8 13.2 - - + -
321A VAL 3.3 5.8 - - - -
322A LEU* 3.4 26.2 - - + -
323A GLN* 6.0 0.2 - - - -
327A ALA* 1.3 75.5 - - - +
329A SER* 1.3 69.5 + - - +
330A TRP* 3.5 39.3 - - + +
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Residues in contact with SER 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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90A PHE* 3.7 15.9 - - - -
247A GLN* 4.3 19.1 + - - -
248A LEU 3.6 5.2 - - - -
249A SER* 2.7 22.3 + - - -
319A ASP 3.8 0.9 - - - +
320A VAL* 3.3 5.7 - - - -
321A VAL* 2.9 47.8 + - - +
323A GLN* 4.6 2.8 + - - -
328A LEU* 1.3 77.5 - - - +
330A TRP* 1.3 61.3 + - - +
331A ARG* 4.7 6.3 + - - +
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Residues in contact with TRP 330 (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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232A LEU* 6.3 0.8 - - - +
246A LEU 3.5 0.7 - - - +
247A GLN* 3.1 27.7 - - - +
248A LEU* 2.9 39.4 + - + +
249A SER* 5.6 0.7 - - - -
250A THR* 5.5 3.6 - - + +
260A LEU* 3.8 23.3 - - + -
296A PRO* 3.4 45.1 - - + -
298A TYR* 3.6 29.5 + + - -
310A VAL* 4.1 19.3 - - + +
312A LEU* 3.6 38.7 - - + +
318A MET* 3.8 4.3 - - - -
319A ASP 4.0 3.1 - - - -
320A VAL* 3.6 20.6 - - + -
328A LEU* 3.5 18.3 - - + +
329A SER* 1.3 70.7 - - - +
331A ARG* 1.3 58.9 + - - +
332A SER 4.0 0.9 - - - -
337A LEU* 5.5 2.8 - - + +
339A VAL* 5.8 2.5 - - + +
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Residues in contact with ARG 331 (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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91A ASP* 4.0 22.8 + - - +
94A PRO* 3.5 27.8 + - - +
122A MET* 5.3 6.5 - - - +
245A PHE* 3.8 21.1 - - + -
246A LEU 3.2 4.9 - - - -
247A GLN* 2.8 29.3 + - + +
275A ARG* 6.0 1.2 - - - +
318A MET* 3.2 6.1 - - - +
319A ASP* 2.8 42.1 + - + +
321A VAL* 3.8 35.3 - - - +
329A SER* 4.7 8.5 + - - +
330A TRP* 1.3 73.9 - - - +
332A SER* 1.3 61.7 + - - +
543A TYR* 3.1 36.3 + - + -
545A PRO* 5.2 0.3 - - - +
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Residues in contact with SER 332 (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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245A PHE* 3.4 7.3 - - - -
246A LEU* 2.9 39.6 + - - -
312A LEU* 5.1 6.1 - - - -
314A ASN* 2.7 38.9 + - - -
316A ASN* 3.4 5.5 - - - +
317A ALA 3.8 4.5 + - - -
318A MET* 3.8 11.6 - - - +
330A TRP* 4.0 1.0 - - - -
331A ARG* 1.3 75.6 - - - +
333A THR* 1.3 66.2 + - - +
334A GLY 3.3 9.4 + - - -
337A LEU* 5.9 0.9 - - - -
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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