Contacts of the strand formed by residues 312 - 320 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B ILE* 3.7 24.0 - - - +
311B ARG* 1.3 87.9 + - - +
313B LEU* 1.3 60.1 + - - +
314B TYR* 3.5 37.3 + - + -
376B ASN* 6.2 0.2 - - - +
377B VAL 3.6 12.6 - - - +
378B ASP* 3.9 10.4 - - - +
379B LEU* 3.9 5.3 - - - +
479B ALA 3.8 0.2 - - - +
480B ILE* 3.3 8.1 - - - +
481B VAL* 2.8 41.4 + - + +
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Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ASN* 1.3 74.4 - - - +
314B TYR* 1.3 62.5 + - - +
315B VAL* 3.8 12.1 + - + -
375B ILE 4.1 0.2 - - - +
376B ASN* 3.3 6.4 - - - +
377B VAL* 2.8 57.9 + - + +
379B LEU* 4.1 13.4 - - + +
387B VAL* 4.2 16.2 - - + -
390B ILE* 4.0 18.6 - - + -
391B ILE* 4.0 18.8 - - + -
394B MET* 4.4 3.8 - - + -
478B VAL* 3.6 26.0 - - + -
479B ALA 3.3 15.5 - - - +
480B ILE* 4.0 9.9 - - + -
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Residues in contact with TYR 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B LEU* 3.7 32.8 - - + +
310B ILE* 5.6 1.6 - - - +
312B ASN* 3.5 37.5 + - + -
313B LEU* 1.3 73.7 - - - +
315B VAL* 1.3 62.5 + - - +
316B THR* 4.0 4.8 - - + +
376B ASN* 3.3 37.7 - - + +
377B VAL 5.7 0.2 - - - -
477B ARG 3.7 1.2 - - - +
478B VAL* 3.5 2.8 - - - -
479B ALA* 2.7 53.7 + - + +
481B VAL* 3.9 16.6 - - + -
2000B DIO 4.0 22.4 - - - -
2002B DIO 4.2 11.9 - - - -
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Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 4.0 12.6 - - + -
314B TYR* 1.3 73.9 - - - +
316B THR* 1.3 65.5 + - - +
317B PHE* 4.1 17.5 - - + -
374B ILE* 3.4 3.1 - - - -
375B ILE* 2.9 45.9 + - + +
376B ASN* 3.4 3.0 + - - +
391B ILE* 3.8 34.1 - - + -
394B MET* 3.9 20.2 - - - -
395B PHE* 5.7 1.6 - - + -
476B VAL* 3.8 23.3 - - + -
477B ARG 3.6 2.2 - - - -
478B VAL* 4.5 4.5 - - + -
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Residues in contact with THR 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B GLU* 3.6 24.1 + - - +
293B PHE* 4.5 6.1 - - - -
314B TYR* 4.0 11.0 - - + +
315B VAL* 1.3 81.9 - - - +
317B PHE* 1.3 63.3 + - - +
318B PRO* 4.3 1.3 - - - +
372B PHE* 4.4 12.3 - - - -
373B PHE 3.5 3.5 + - - -
374B ILE* 3.8 17.8 - - - +
376B ASN* 5.4 0.9 - - - +
475B ASN 4.1 0.2 - - - +
476B VAL* 3.8 2.3 - - - -
477B ARG* 2.9 55.4 + - + +
2000B DIO 5.8 1.1 - - - -
2002B DIO 4.0 16.8 - - - +
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Residues in contact with PHE 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B PHE* 5.8 0.2 - - - -
315B VAL* 4.1 15.9 - - + -
316B THR* 1.3 77.5 + - - +
318B PRO* 1.3 70.9 - - + +
372B PHE* 3.4 4.9 - - - +
373B PHE* 2.7 54.0 + + + +
375B ILE* 4.8 16.8 - - + -
395B PHE* 3.6 23.1 - + - -
398B ILE* 4.9 3.8 - - + -
470B LYS 4.5 1.3 - - - +
471B LEU* 3.7 44.9 - - + -
472B ARG 3.7 23.6 - - - -
475B ASN* 3.4 18.8 - - - -
476B VAL* 3.6 23.6 - - + -
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Residues in contact with PRO 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B HIS* 3.4 36.3 - - + +
293B PHE* 4.5 13.2 - - + +
298B LEU* 3.6 24.0 - - + -
316B THR 4.3 2.2 - - - +
317B PHE* 1.3 85.5 - - - +
319B ILE* 1.3 68.1 + - - +
371B MET 3.9 0.9 - - - +
372B PHE* 4.7 1.8 - - + -
470B LYS* 4.3 5.5 - - - +
475B ASN* 3.1 46.7 + - + +
477B ARG* 5.5 1.3 - - - +
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Residues in contact with ILE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B HIS* 3.3 12.6 - - - -
317B PHE 4.3 0.4 - - - +
318B PRO* 1.3 84.2 - - - +
320B PRO* 1.4 75.1 - - + +
322B LEU* 3.7 28.9 - - + -
363B GLN* 4.7 0.7 - - + -
370B PHE* 4.0 0.3 - - - -
371B MET* 3.0 51.4 + - + +
372B PHE 3.5 23.3 - - - +
373B PHE* 4.0 23.8 - - + -
467B VAL* 4.8 7.9 - - + -
470B LYS* 4.1 19.3 - - + +
471B LEU* 4.4 8.1 - - + -
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Residues in contact with PRO 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B HIS* 5.4 0.7 - - + -
319B ILE* 1.4 93.1 - - + +
321B ASP* 1.3 70.5 + - - +
322B LEU* 2.8 22.1 + - + +
325B TYR* 6.2 2.2 - - + -
369B GLY 4.5 5.4 - - - +
371B MET* 4.1 0.6 - - - +
466B MET* 4.2 23.8 - - + -
470B LYS* 3.7 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
------------------------------------------------------------
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