Contacts of the strand formed by residues 316 - 325 (chain A) in PDB entry 5C7Z
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 LEU 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311A PHE* 4.5 1.3 - - - -
314A SER 4.2 3.5 + - - +
315A LEU* 1.3 74.1 - - - +
317A ALA* 1.3 65.5 + - - +
318A GLN* 4.0 8.7 + - + +
357A ARG* 3.9 30.1 - - + -
358A MET* 3.6 9.0 - - - +
359A ALA* 3.5 35.0 - - + +
393A PRO* 3.1 25.8 - - - +
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Residues in contact with ALA 317 (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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287A PHE* 3.8 28.3 - - + -
311A PHE* 3.8 12.6 - - + -
316A LEU* 1.3 75.8 - - - +
318A GLN* 1.3 62.8 + - - +
320A ILE* 4.0 8.7 - - + -
357A ARG* 3.3 5.7 - - - -
358A MET 2.8 37.5 + - - +
390A PHE* 5.0 0.2 - - + -
391A GLU 3.4 13.5 - - - +
392A VAL* 4.0 8.5 - - + -
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Residues in contact with GLN 318 (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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316A LEU* 4.4 10.3 - - + +
317A ALA* 1.3 78.1 - - - +
319A LYS* 1.3 75.7 + - + +
320A ILE* 3.5 4.5 + - - +
356A LYS 3.4 9.3 - - - +
357A ARG* 3.2 37.3 + - + +
390A PHE* 3.9 1.4 - - - -
391A GLU* 3.0 47.1 + - + +
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Residues in contact with LYS 319 (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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318A GLN* 1.3 84.2 - - + +
320A ILE* 1.3 61.2 + - - +
321A GLU* 3.7 2.0 + - - +
355A ILE 4.1 2.7 - - - -
356A LYS* 3.2 14.5 + - - +
389A ASN* 3.4 13.7 - - - +
390A PHE* 3.4 6.6 + - - -
391A GLU* 2.8 44.1 + - + +
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Residues in contact with ILE 320 (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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287A PHE* 4.1 7.2 - - + -
307A ILE* 4.3 4.9 - - + -
317A ALA* 4.0 17.9 - - + +
318A GLN 3.9 8.7 - - - +
319A LYS* 1.3 76.9 - - - +
321A GLU* 1.3 64.5 + - - +
322A VAL* 4.6 1.8 - - + -
353A TRP 3.9 0.2 - - - +
354A LYS* 3.3 4.5 - - - +
355A ILE* 2.8 65.8 + - + +
357A ARG 4.2 0.2 - - - -
358A MET* 3.6 37.9 - - + +
388A MET* 3.6 29.2 - - + -
389A ASN 3.2 4.0 - - - +
390A PHE* 4.1 10.5 - - + -
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Residues in contact with GLU 321 (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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319A LYS 3.7 2.2 + - - +
320A ILE* 1.3 75.2 - - - +
322A VAL* 1.3 68.8 + - - +
323A ARG* 2.9 34.1 + - + +
352A VAL* 4.0 17.2 - - + +
353A TRP 3.2 6.5 - - - +
354A LYS* 3.7 22.3 - - + -
388A MET* 3.2 6.8 - - - +
389A ASN* 2.8 55.5 + - + +
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Residues in contact with VAL 322 (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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289A VAL* 5.3 0.4 - - + -
305A VAL* 4.6 10.1 - - + -
307A ILE* 4.1 15.5 - - + -
320A ILE* 4.6 3.6 - - + -
321A GLU* 1.3 77.7 - - - +
323A ARG* 1.3 63.8 + - - +
324A ILE* 4.0 11.0 + - + +
351A ILE 3.5 3.3 - - - +
352A VAL* 3.5 1.4 - - - +
353A TRP* 2.8 64.5 + - + +
355A ILE* 5.3 0.7 - - + -
386A ILE* 3.7 24.9 - - + -
387A SER 3.5 4.5 - - - +
388A MET* 4.0 24.5 - - + +
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Residues in contact with ARG 323 (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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321A GLU* 2.9 35.3 + - + +
322A VAL* 1.3 74.7 - - - +
324A ILE* 1.3 59.1 + - - +
325A PRO* 3.7 3.8 - - + +
345A LYS* 5.8 0.2 - - - +
348A GLU* 2.4 44.7 + - - +
350A ALA* 4.2 15.3 - - + +
351A ILE 3.4 5.2 - - - +
352A VAL* 3.6 17.6 - - + +
385A PRO 5.9 0.7 - - - +
386A ILE* 3.3 9.4 - - - +
387A SER* 2.8 51.3 + - - +
389A ASN* 6.3 0.7 - - - +
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Residues in contact with ILE 324 (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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303A VAL* 4.4 22.4 - - + -
305A VAL* 3.9 26.2 - - + -
322A VAL* 4.3 10.5 - - + +
323A ARG* 1.3 75.6 - - - +
325A PRO* 1.3 76.5 - - + +
326A THR* 3.9 1.1 - - + +
350A ALA* 3.2 1.7 - - - -
351A ILE* 2.7 67.4 + - + +
353A TRP* 5.5 1.3 - - + -
366A ILE* 3.9 22.9 - - + -
370A ILE* 5.8 2.0 - - + -
386A ILE* 4.3 17.3 - - + -
435A CYS* 6.4 0.4 - - - -
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Residues in contact with PRO 325 (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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323A ARG* 3.7 6.7 - - + +
324A ILE* 1.3 95.8 - - + +
326A THR* 1.3 61.2 + - - +
349A ASN 3.5 11.0 - - - +
350A ALA* 4.1 4.7 - - + -
370A ILE* 5.2 2.6 - - - +
381A TRP* 3.2 16.1 - - + -
384A PRO* 3.4 51.1 - - + +
385A PRO 3.5 18.6 - - - +
386A ILE* 4.2 7.0 - - + -
435A CYS* 5.5 2.5 - - - -
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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