Contacts of the strand formed by residues 320 - 326 (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 PHE 320 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A VAL* 4.1 24.0 - - + -
278A LEU* 4.5 10.1 - - + -
281A ILE* 4.4 15.9 - - + -
287A TYR* 4.0 19.5 - + - -
310A LEU* 4.0 9.9 - - + -
311A ARG 3.3 12.6 - - - +
312A ASP* 3.7 16.4 - - - -
313A SER* 3.7 5.3 - - - +
318A TYR* 3.5 1.1 - - - +
319A LEU* 1.3 98.3 - - + +
321A SER* 1.3 64.9 + - - +
334A ARG* 3.9 1.4 - - - +
335A ILE* 3.1 44.1 + - + +
342A PHE* 6.2 0.2 - + - -
357A ILE* 4.1 25.4 - - + -
422A TYR* 4.0 24.7 - + - -
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Residues in contact with SER 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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310A LEU* 3.4 5.9 - - - +
311A ARG* 2.9 64.3 + - - +
313A SER* 3.2 23.7 + - - +
315A GLN* 5.3 1.0 + - - -
320A PHE* 1.3 71.5 + - - +
322A VAL* 1.3 65.5 + - - +
332A HIS* 5.5 0.9 - - - -
333A ALA 3.3 14.1 - - - -
334A ARG* 3.7 11.3 + - - +
335A ILE* 4.4 0.7 - - - +
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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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308A PHE* 5.0 1.6 - - + -
309A LEU 3.2 10.3 - - - +
310A LEU* 3.9 11.2 - - + -
321A SER* 1.3 77.6 - - - +
323A SER* 1.3 63.5 + - - +
324A PHE* 3.9 14.8 - - + -
332A HIS* 3.3 4.9 - - - +
333A ALA* 2.9 56.8 + - + +
335A ILE* 4.7 1.5 - - + +
344A PHE* 3.9 16.8 - - + -
361A LEU* 3.7 31.0 - - + -
375A PRO* 4.7 1.1 - - + -
377A LEU* 4.2 16.8 - - + -
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Residues in contact with SER 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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296A ALA* 3.5 13.1 - - - +
300A LEU* 3.6 19.0 - - - +
308A PHE* 3.2 3.5 - - - +
309A LEU* 2.9 40.1 + - - +
311A ARG* 3.0 18.5 + - - -
322A VAL* 1.3 71.8 - - - +
324A PHE* 1.3 61.5 + - - +
331A LEU 3.4 4.9 - - - -
332A HIS* 2.7 28.8 + - - -
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Residues in contact with PHE 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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300A LEU* 3.7 5.0 - - - +
307A THR 3.3 6.7 - - - +
308A PHE* 3.6 17.0 - - + -
322A VAL* 3.9 14.1 - - + -
323A SER* 1.3 78.9 - - - +
325A ARG* 1.3 69.7 + - - +
326A ARG* 4.1 10.3 - - + -
329A ARG 3.6 0.3 - - - +
330A SER* 3.6 3.5 - - - -
331A LEU* 2.8 78.0 + - + +
332A HIS 4.4 1.8 - - - -
333A ALA* 4.2 13.7 - - + -
374A GLU 4.9 1.8 - - - -
375A PRO* 3.6 28.5 - - + -
376A LEU 3.7 24.2 - - - +
377A LEU* 3.7 10.3 - - + -
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Residues in contact with ARG 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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300A LEU* 3.6 25.2 + - + +
301A GLU* 4.5 2.2 - - - +
302A GLY* 3.5 26.7 + - - +
303A LYS* 3.0 26.6 + - + +
304A PRO 3.6 19.3 - - - +
305A GLU* 4.2 1.7 - - - +
306A GLY* 2.8 25.9 + - - +
307A THR* 3.0 13.1 + - - +
324A PHE* 1.3 82.3 - - - +
326A ARG* 1.3 66.5 + - - +
328A SER* 3.4 40.6 + - - +
329A ARG* 3.6 7.8 + - - +
330A SER* 3.5 23.9 + - - +
376A LEU* 4.4 0.7 - - - +
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Residues in contact with ARG 326 (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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305A GLU* 3.9 29.1 + - + +
324A PHE* 4.1 7.6 + - + -
325A ARG* 1.3 77.2 - - - +
327A TYR* 1.3 102.6 + - + +
328A SER 3.1 2.5 - - - +
329A ARG* 3.0 29.5 + - - +
331A LEU* 3.7 20.0 - - + +
367A PRO 5.0 2.4 + - - -
370A CYS* 3.5 28.1 + - - +
371A MET 3.0 15.1 + - - -
372A PHE* 3.9 4.0 + - - +
374A GLU 2.7 33.4 + - - -
376A LEU* 4.0 27.6 - - - +
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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