Contacts of the strand formed by residues 331 - 337 (chain A) in PDB entry 3FZF
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 ILE 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A ASN* 4.0 12.1 - - + +
195A VAL 4.8 0.9 - - - +
196A LEU* 4.3 16.8 - - + +
209A ILE* 4.4 9.9 - - + -
321A LEU* 3.0 37.9 - - + -
326A LEU* 4.5 10.3 - - + -
327A ASP 4.3 4.3 - - - +
328A LYS* 3.7 5.2 + - - +
329A SER 3.3 8.4 - - - +
330A GLN* 1.3 77.1 - - - +
332A HIS* 1.3 63.7 + - - +
333A ASP 3.7 21.3 - - - +
334A ILE* 3.9 21.8 - - + -
354A PHE* 4.1 18.6 - - + -
357A LYS* 4.0 12.8 - - - +
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Residues in contact with HIS 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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192A GLU 4.1 9.1 + - - -
193A ARG* 3.3 25.3 - - + +
194A ASN* 2.6 50.0 + - - +
329A SER 5.8 0.6 + - - -
330A GLN* 3.0 27.6 + - + +
331A ILE* 1.3 75.1 - - - +
333A ASP* 1.3 73.3 + - - +
357A LYS* 4.1 4.9 - - - +
358A GLU* 3.8 17.7 + - - +
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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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185A LEU* 3.9 8.6 - - + +
188A LYS* 3.4 27.4 + - - +
193A ARG* 4.0 11.8 + - - -
194A ASN 3.4 2.4 + - - -
195A VAL* 3.2 22.9 - - + +
196A LEU 2.8 31.9 + - - +
331A ILE* 3.7 3.9 - - - +
332A HIS* 1.3 94.2 - - - +
334A ILE* 1.3 60.0 + - - +
335A VAL 4.2 0.2 - - - -
358A GLU* 3.6 14.2 - - - +
360A ASN* 3.3 22.7 + - - +
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Residues in contact with ILE 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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196A LEU* 3.2 24.9 - - + +
198A PHE* 4.5 2.7 - - + -
331A ILE* 3.9 8.7 - - + -
333A ASP* 1.3 80.8 - - - +
335A VAL* 1.3 59.0 + - - +
336A LEU* 4.4 11.2 - - + -
350A LEU* 4.7 4.0 - - + -
351A GLN* 6.2 0.2 - - - +
354A PHE* 3.5 50.5 - - + -
357A LYS* 3.6 21.1 - - + +
358A GLU 3.0 12.9 + - - +
359A LEU* 3.4 28.0 - - + -
360A ASN* 2.7 35.0 + - - +
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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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179A ALA* 4.1 12.1 - - + +
180A ALA* 4.9 4.0 - - - -
183A TYR* 3.6 31.0 - - + -
185A LEU* 3.8 29.2 - - + -
195A VAL* 4.1 12.1 - - + -
196A LEU 2.9 5.7 + - - -
197A ILE* 3.5 14.5 - - + +
198A PHE* 2.9 28.9 + - - +
334A ILE* 1.3 77.7 - - - +
336A LEU* 1.3 64.2 + - - +
337A VAL* 4.0 16.6 - - + -
360A ASN* 3.3 10.8 - - + +
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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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183A TYR* 4.5 7.4 + - - -
198A PHE* 3.6 21.8 - - + -
334A ILE* 4.4 1.1 - - + -
335A VAL* 1.3 74.3 - - - +
337A VAL* 1.3 70.3 + - - +
341A THR* 3.8 22.1 + - + +
346A ILE* 6.1 0.7 - - + -
347A GLN* 3.7 32.1 - - + -
350A LEU* 3.7 26.9 - - + -
359A LEU* 4.0 22.9 - - + -
360A ASN 2.8 15.9 + - - +
361A LYS* 3.7 29.6 - - + -
363A ILE 5.2 0.5 - - - +
365A PRO* 4.4 8.0 - - + +
368A ALA* 5.2 1.0 - - - +
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Residues in contact with VAL 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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179A ALA* 3.7 28.0 - - + -
197A ILE* 4.2 9.4 - - + -
198A PHE 3.0 6.2 + - - +
199A ASP* 3.1 39.0 - - + +
200A LEU 3.1 21.7 + - - -
335A VAL* 4.0 9.0 - - + -
336A LEU* 1.3 80.7 - - - +
338A GLY* 1.3 63.1 + - - +
341A THR* 3.2 5.9 - - - +
365A PRO* 3.7 15.0 - - - +
368A ALA* 4.2 12.1 - - + -
369A VAL* 4.6 14.6 - - + -
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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