Contacts of the strand formed by residues 333 - 336 (chain C) in PDB entry 1V1H
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 ALA 333 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320A SER* 3.3 26.9 + - - +
321A ILE 3.8 16.6 - - - +
322A LYS* 3.9 9.6 - - + +
329C PHE* 3.2 5.9 - - - -
330C ASP* 2.8 39.3 + - - +
331C ASN* 3.1 7.4 + - + +
332C THR* 1.3 77.2 - - - +
334C ILE* 1.3 63.6 + - - +
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Residues in contact with ILE 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A VAL* 4.1 11.9 - - + -
320A SER 2.9 14.3 + - - +
321A ILE* 4.3 3.1 - - + -
322A LYS 2.8 27.4 + - - -
327A LEU* 3.4 24.3 - - + +
334A ILE* 4.3 8.7 - - + -
334B ILE* 4.1 12.3 - - + -
319C VAL* 4.0 27.1 - - + -
321C ILE* 3.9 27.6 - - + -
327C LEU* 4.4 18.6 - - + -
328C ASN 3.7 7.2 - - - +
329C PHE* 3.8 20.2 - - + -
333C ALA* 1.3 70.3 - - - +
335C ALA* 1.3 61.1 + - - +
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Residues in contact with ALA 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A LYS* 4.1 13.7 - - + -
325A SER* 3.8 23.6 - - - +
327A LEU* 4.0 7.0 - - - -
327C LEU* 3.5 6.0 - - - +
328C ASN* 2.9 38.1 + - + +
330C ASP* 4.1 12.6 - - + +
333C ALA 3.5 0.2 + - - -
334C ILE* 1.3 75.2 - - - +
336C ILE* 1.3 67.0 + - - +
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Residues in contact with ILE 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A SER* 3.3 16.5 + - - +
326A GLY* 3.4 29.2 - - - +
327A LEU* 3.8 20.8 - - + +
336A ILE* 4.0 21.8 - - + -
357A ILE* 6.2 0.2 - - + -
336B ILE* 3.9 5.4 - - + -
357B ILE* 3.7 22.7 - - + -
326C GLY 3.6 10.8 - - - +
327C LEU* 4.0 10.3 - - + -
328C ASN* 5.9 0.2 - - - -
335C ALA* 1.3 78.5 - - - +
337C ASN* 1.3 63.0 + - - +
338C ALA 3.5 1.6 + - - +
344C PHE* 3.3 21.9 - - + -
357C ILE* 3.8 26.0 - - + -
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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