Contacts of the strand formed by residues 330 - 337 (chain A) in PDB entry 3F7F
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 SER 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295A ASN* 4.5 1.6 - - - +
328A ILE 4.8 2.1 + - - -
329A TRP* 1.3 75.6 + - - +
331A ILE* 1.3 67.1 + - - +
332A VAL* 3.4 1.8 + - - +
355A TRP* 3.1 5.8 - - - -
356A LYS* 2.8 42.2 + - - -
357A SER* 5.4 0.5 - - - -
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Residues in contact with ILE 331 (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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277A GLY* 5.7 0.4 - - - -
278A GLU 3.8 28.4 + - - +
279A TYR* 3.9 21.3 - - + +
290A LEU* 3.5 30.1 - - + -
295A ASN* 4.8 1.6 + - - +
298A PHE* 4.5 4.0 - - + -
330A SER* 1.3 77.2 - - - +
332A VAL* 1.3 59.0 + - - +
333A ASP 4.2 10.3 - - - +
334A LEU* 4.4 7.9 - - + -
353A VAL* 3.3 33.7 - - + -
354A LEU 3.7 8.7 - - - +
355A TRP* 3.5 18.5 - - + -
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Residues in contact with VAL 332 (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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105A ARG* 4.7 5.9 + - - -
278A GLU* 3.5 16.0 + - - +
330A SER* 3.8 0.4 - - - +
331A ILE* 1.3 76.4 - - - +
333A ASP* 1.3 61.3 + - - +
354A LEU* 2.7 38.5 + - + +
355A TRP 3.6 7.6 - - - +
356A LYS* 3.3 42.6 - - + +
460A ALA* 3.9 6.5 - - + +
461A SER* 3.3 42.1 - - - +
462A SER 4.1 0.2 - - - +
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Residues in contact with ASP 333 (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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58A ASN* 4.9 3.1 + - - -
278A GLU* 4.0 25.8 - - - +
331A ILE* 3.8 3.4 - - - +
332A VAL* 1.3 84.2 - - + +
334A LEU* 1.3 87.1 + - - +
335A VAL* 5.8 0.4 - - - -
354A LEU* 3.0 26.4 + - + +
462A SER* 3.7 14.5 - - - -
463A ILE* 3.1 50.8 + - + +
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Residues in contact with LEU 334 (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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278A GLU* 3.4 26.6 - - + +
279A TYR* 4.1 5.4 - - - +
280A LEU* 3.9 13.0 - - - +
281A SER* 3.0 48.8 + - - +
288A VAL* 4.4 4.3 - - + -
289A THR 5.9 0.2 - - - -
290A LEU* 4.7 2.5 - - + -
298A PHE* 4.0 22.4 - - + -
331A ILE* 4.4 12.6 - - + -
333A ASP* 1.3 87.6 + - - +
335A VAL* 1.3 65.1 + - - +
351A LEU* 4.3 14.1 - - + -
352A ILE 3.2 11.2 - - - +
353A VAL* 4.7 6.3 - - + -
463A ILE* 4.2 0.2 - - - -
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Residues in contact with VAL 335 (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 SER* 3.9 3.6 - - - -
333A ASP* 5.3 0.9 - - - +
334A LEU* 1.3 79.0 - - - +
336A LEU* 1.3 69.9 + - - +
337A THR* 3.7 3.4 + - + +
350A ASN 3.7 0.7 - - - +
351A LEU* 3.7 3.7 - - - +
352A ILE* 2.9 58.7 + - + +
463A ILE* 3.6 26.0 - - + -
465A LEU* 3.5 29.8 - - + -
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Residues in contact with LEU 336 (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 SER* 3.2 31.1 + - - +
282A LEU 4.7 2.4 - - - +
283A TYR* 4.0 38.2 + - + +
286A THR* 4.2 21.3 - - + +
288A VAL* 3.6 27.4 - - + +
300A MET* 6.4 0.4 - - - -
335A VAL* 1.3 74.2 - - - +
337A THR* 1.3 65.0 + - - +
349A LEU* 4.3 21.5 - - + -
350A ASN 3.5 22.2 - - - +
351A LEU* 3.7 17.0 - - + +
368A VAL* 6.5 0.2 - - + -
373A PHE* 6.4 0.2 - - + -
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Residues in contact with THR 337 (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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283A TYR* 3.8 13.7 - - - -
335A VAL* 4.3 6.7 - - - +
336A LEU* 1.3 78.9 - - - +
338A ARG* 1.3 99.3 + - - +
349A LEU* 3.6 10.3 - - - +
350A ASN* 2.8 39.9 + - + +
352A ILE* 4.4 14.6 - - + -
465A LEU* 4.3 28.3 - - + +
468A ASP 5.3 2.3 + - - -
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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