Contacts of the strand formed by residues 307 - 312 (chain A) in PDB entry 2IZV
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 THR 307 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A LEU* 3.6 22.4 - - + +
303A LYS* 4.1 15.9 - - + +
304A PRO* 2.8 35.6 + - - +
305A GLU 3.4 0.7 + - - -
306A GLY* 1.3 75.0 - - - +
308A PHE* 1.3 60.3 + - - +
324A PHE* 3.3 2.4 - - - -
325A ARG* 3.0 24.0 + - - +
379A THR* 3.2 22.8 - - + +
381A LEU* 3.6 26.2 - - + -
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Residues in contact with PHE 308 (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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286A CYS* 3.7 32.3 - - + -
300A LEU* 4.4 3.1 - - - -
306A GLY 4.0 1.3 - - - +
307A THR* 1.3 76.0 - - - +
309A LEU* 1.3 73.3 + - - +
310A LEU* 5.3 0.2 - - + -
322A VAL* 5.0 1.8 - - + -
323A SER 3.2 12.3 - - - +
324A PHE* 3.6 12.8 - - + -
361A LEU* 4.4 18.6 - - + -
377A LEU* 3.3 55.9 - - + -
378A SER 3.8 0.4 - - - -
379A THR 3.0 15.6 + - - -
380A PRO* 3.6 28.5 - - + +
381A LEU* 2.8 30.0 + - - +
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Residues in contact with LEU 309 (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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286A CYS 3.6 13.7 - - - +
288A TRP* 3.6 20.6 - - + +
291A MET* 4.2 6.7 - - - -
296A ALA* 4.2 8.3 - - + +
299A LEU* 3.9 31.6 - - + -
300A LEU* 4.8 4.0 - - + -
308A PHE* 1.3 85.0 - - - +
310A LEU* 1.3 60.9 + - - +
311A ARG* 3.8 29.4 - - + -
322A VAL* 3.2 7.6 - - - +
323A SER* 2.9 53.4 + - - +
381A LEU* 4.4 13.0 - - + +
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Residues in contact with LEU 310 (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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281A ILE* 3.9 29.4 - - + -
284A ASN* 6.4 0.7 - - + -
286A CYS* 3.0 21.7 + - - +
287A TYR* 3.8 14.6 - - + -
288A TRP* 2.9 27.9 + - - +
308A PHE* 4.4 1.4 - - - -
309A LEU* 1.3 72.7 - - - +
311A ARG* 1.3 65.8 + - - +
320A PHE* 4.0 11.0 - - + -
321A SER 3.4 16.4 - - - +
322A VAL* 3.9 10.3 - - + -
335A ILE* 3.9 26.2 - - + -
357A ILE* 4.0 18.4 - - + -
361A LEU* 4.1 15.0 - - + -
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Residues in contact with ARG 311 (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 TYR* 4.1 7.4 - - - -
288A TRP* 4.8 1.6 - - + -
289A GLY 3.6 12.6 - - - +
291A MET* 3.2 41.8 + - + -
292A ASP* 3.9 6.2 - - - +
293A LYS* 3.6 19.6 - - - +
296A ALA* 3.8 5.2 - - - +
309A LEU* 3.8 18.2 - - + -
310A LEU* 1.3 77.3 - - - +
312A ASP* 1.3 72.9 + - - +
313A SER* 4.1 9.5 - - - +
314A ALA* 4.6 3.0 - - - +
320A PHE* 3.3 7.3 - - - +
321A SER* 2.9 52.1 + - - +
323A SER* 3.0 16.2 + - - -
332A HIS* 3.2 29.1 + - - +
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Residues in contact with ASP 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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287A TYR* 2.5 29.7 + - - -
289A GLY 2.9 19.3 + - - +
290A VAL* 3.8 11.3 - - + +
291A MET 3.2 22.3 + - - +
311A ARG* 1.3 78.2 + - - +
313A SER* 1.3 61.6 + - - +
319A LEU 3.2 7.6 - - - -
320A PHE* 3.7 5.4 - - - -
422A TYR* 2.5 33.5 + - - -
1431A EDO 2.8 27.0 + - - +
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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