Contacts of the strand formed by residues 311 - 318 (chain A) in PDB entry 2IN6
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 GLY 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A SER* 3.8 1.4 - - - -
308A GLY* 3.1 29.0 + - - -
310A PHE* 1.3 76.4 - - - +
312A SER* 1.3 63.4 + - - -
313A VAL* 5.4 1.4 - - - +
328A LYS* 4.9 5.3 - - - +
329A ARG 3.2 16.2 - - - -
330A SER* 3.8 7.2 - - - +
331A LYS 5.2 0.8 - - - +
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Residues in contact with SER 312 (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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304A LYS* 3.5 20.7 + - - -
306A GLY 3.3 13.7 - - - -
307A SER* 3.9 7.6 + - - -
311A GLY* 1.3 77.0 + - - -
313A VAL* 1.3 63.8 + - - +
314A PHE* 3.5 30.4 - - - -
328A LYS* 3.3 1.7 - - - +
329A ARG 2.8 32.9 + - - +
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Residues in contact with VAL 313 (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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304A LYS* 3.6 4.3 - - - +
305A ILE* 2.8 48.5 + - + -
306A GLY* 3.0 18.8 + - - +
311A GLY 5.4 1.1 - - - +
312A SER* 1.3 77.5 - - - +
314A PHE* 1.3 59.1 + - - +
326A ALA* 4.0 17.5 - - + -
327A ILE 3.3 12.6 - - - +
328A LYS* 4.0 19.1 - - + -
901A 839 3.9 42.2 - - + -
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Residues in contact with PHE 314 (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 TYR* 3.6 25.8 - + - +
301A GLU* 3.6 33.0 - - + -
303A GLU 3.3 6.5 - - - +
304A LYS* 3.5 42.4 - - + -
305A ILE* 4.3 4.3 - - - -
312A SER* 3.5 37.2 - - - -
313A VAL* 1.3 75.1 - - - +
315A LYS* 1.3 61.1 + - - +
316A CYS* 3.6 5.2 + - - -
325A TYR 3.5 0.7 - - - +
326A ALA* 3.5 3.8 - - - -
327A ILE* 2.9 36.9 + - - +
329A ARG* 4.3 19.7 - - + -
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Residues in contact with LYS 315 (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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301A GLU 3.7 0.2 - - - -
302A LEU* 2.7 57.5 + - + +
303A GLU* 2.8 41.4 + - + +
305A ILE* 3.9 18.9 - - + +
314A PHE* 1.3 71.4 - - - +
316A CYS* 1.3 53.0 + - - +
324A ILE* 3.6 29.6 - - + +
325A TYR 3.6 4.0 - - - -
378A TYR* 3.7 40.5 + - + +
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Residues in contact with CYS 316 (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 TYR* 3.4 38.6 - - - -
299A PHE* 4.0 11.0 - - + -
300A HIS 3.2 10.1 - - - +
301A GLU* 3.9 10.3 - - - -
302A LEU* 4.5 0.4 - - - -
314A PHE* 3.9 11.2 - - - -
315A LYS* 1.3 80.8 - - - +
317A VAL* 1.3 63.6 + - - +
318A LYS 4.0 0.6 + - - -
323A CYS 3.8 0.3 - - - +
324A ILE* 3.3 4.7 - - - -
325A TYR* 2.8 34.6 + - - +
327A ILE* 3.9 21.5 - - + -
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Residues in contact with VAL 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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299A PHE* 3.3 3.1 - - - -
300A HIS* 2.8 48.5 + - + +
302A LEU* 3.5 36.6 - - + -
316A CYS* 1.3 73.2 - - - +
318A LYS* 1.3 72.4 + - - +
319A ARG* 3.4 2.7 + - - -
322A GLY* 3.9 18.4 - - - +
323A CYS 3.4 11.0 - - - +
324A ILE* 4.3 10.1 - - + -
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Residues in contact with LYS 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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298A GLU* 3.5 36.0 + - - +
299A PHE* 3.5 28.9 - - + -
316A CYS 4.0 0.6 + - - -
317A VAL* 1.3 72.4 - - - +
319A ARG* 1.3 69.0 + - - +
320A LEU* 4.0 24.5 - - - +
321A ASP* 3.4 34.1 - - - +
322A GLY* 3.0 25.1 + - - -
323A CYS 2.9 8.3 + - - -
325A TYR* 3.7 11.4 - - + +
375A GLN* 4.2 7.0 - - - +
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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