Contacts of the strand formed by residues 312 - 320 (chain A) in PDB entry 3H44
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 ASN 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A ILE* 3.9 27.9 - - - +
311A ARG* 1.3 80.4 - - - +
313A LEU* 1.3 60.3 + - - +
314A TYR* 3.3 36.6 + - + -
377A VAL 3.5 5.7 - - - +
378A ASP* 3.3 21.0 + - - +
379A LEU* 3.6 10.1 - - - +
479A ALA 3.6 0.3 - - - +
480A ILE* 3.3 4.9 - - - -
481A VAL* 2.7 44.9 + - + +
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Residues in contact with LEU 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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312A ASN* 1.3 74.2 - - - +
314A TYR* 1.3 62.4 + - - +
315A VAL* 3.9 14.5 + - + -
375A ILE 4.0 0.5 - - - +
376A ASN* 3.3 5.2 - - - +
377A VAL* 3.0 45.4 + - + +
379A LEU* 3.8 17.6 - - + +
387A VAL* 3.8 25.4 - - + -
390A ILE* 3.9 29.4 - - + -
391A ILE* 4.3 7.2 - - + -
394A MET* 5.0 0.9 - - + -
478A VAL* 3.6 25.8 - - + -
479A ALA 3.3 13.9 - - - +
480A ILE* 4.3 3.4 - - + +
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Residues in contact with TYR 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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201A LEU* 3.6 22.6 - - + +
312A ASN* 3.3 35.7 + - + -
313A LEU* 1.3 71.8 - - - +
315A VAL* 1.3 62.2 + - - +
316A THR* 4.0 6.2 + - + +
376A ASN* 3.3 37.5 - - + +
377A VAL 6.1 0.2 - - - -
477A ARG 3.7 1.2 - - - +
478A VAL* 3.6 4.0 - - - -
479A ALA* 2.8 48.4 + - + +
481A VAL* 3.5 31.4 - - + -
2000A DIO 4.2 23.1 - - - -
2002A DIO 4.7 10.8 - - - -
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Residues in contact with VAL 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LEU* 4.1 19.5 - - + -
314A TYR* 1.3 73.6 - - - +
316A THR* 1.3 64.2 + - - +
317A PHE* 3.9 18.9 - - + -
374A ILE* 3.4 2.9 - - - -
375A ILE* 2.8 49.0 + - + +
376A ASN* 3.5 3.0 + - - +
391A ILE* 4.2 17.0 - - + -
394A MET* 3.9 28.3 - - + -
395A PHE* 5.6 0.7 - - + -
476A VAL* 3.7 25.4 - - + -
477A ARG 3.5 2.7 - - - +
478A VAL* 4.8 2.7 - - + -
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Residues in contact with THR 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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205A GLU* 4.1 16.7 + - - +
293A PHE* 4.5 6.1 - - - -
314A TYR* 4.2 10.1 - - + +
315A VAL* 1.3 78.1 - - - +
317A PHE* 1.3 63.0 + - - +
318A PRO* 4.3 0.5 - - - +
372A PHE* 4.2 15.8 - - - -
373A PHE 3.7 2.9 - - - -
374A ILE* 3.7 17.5 - - + +
376A ASN* 5.8 0.2 - - - +
475A ASN 4.2 0.2 - - - +
476A VAL* 3.8 0.7 - - - -
477A ARG* 2.8 55.8 + - + +
2000A DIO 6.1 0.7 - - - -
2002A DIO 3.9 23.8 - - - +
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Residues in contact with PHE 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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315A VAL* 3.9 23.8 - - + -
316A THR* 1.3 76.9 - - - +
318A PRO* 1.3 68.6 - - + +
372A PHE* 3.4 4.0 - - - +
373A PHE* 2.8 47.5 + + - +
375A ILE* 4.3 18.8 - - + -
395A PHE* 3.7 27.6 - + - -
398A ILE* 4.5 4.0 - - + -
470A LYS 3.7 2.5 - - - -
471A LEU* 3.5 43.5 - - + -
472A ARG 3.4 33.7 - - - -
475A ASN* 4.0 13.5 - - - +
476A VAL* 4.0 7.0 - - + -
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Residues in contact with PRO 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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291A HIS* 3.1 38.6 - - + +
293A PHE* 4.5 13.2 - - + +
298A LEU* 3.8 18.8 - - + -
316A THR 4.3 2.7 - - - +
317A PHE* 1.3 82.6 - - - +
319A ILE* 1.3 65.6 + - - +
371A MET 3.8 1.3 - - - +
372A PHE* 4.6 2.2 - - + -
470A LYS* 4.1 6.9 - - - +
475A ASN* 3.3 47.6 - - - +
477A ARG* 5.1 1.1 - - - -
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Residues in contact with ILE 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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291A HIS* 3.3 9.4 + - - -
317A PHE 4.3 0.7 - - - +
318A PRO* 1.3 80.4 - - - +
320A PRO* 1.3 72.1 - - + +
322A LEU* 3.9 26.5 - - + -
363A GLN* 4.6 2.9 - - + -
371A MET* 2.9 56.3 + - + +
372A PHE 3.3 24.0 - - - +
373A PHE* 3.9 21.3 - - + +
467A VAL* 4.6 10.5 - - + -
470A LYS* 4.1 19.5 - - + -
471A LEU* 4.4 7.4 - - + -
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Residues in contact with PRO 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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291A HIS* 5.1 1.8 - - + -
319A ILE* 1.3 94.9 - - + +
321A ASP* 1.3 62.9 + - - +
322A LEU* 2.9 27.8 + - + +
325A TYR* 6.3 1.3 - - + -
369A GLY 4.2 7.6 - - - +
371A MET* 3.7 7.0 - - - +
466A MET* 3.6 31.9 - - + -
467A VAL* 6.4 0.4 - - + -
470A LYS* 4.6 13.5 - - + +
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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