Contacts of the strand formed by residues 330 - 333 (chain C) in PDB entry 1XV9
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 LEU 330 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C TYR* 3.8 1.4 - - - -
250C VAL* 3.1 23.3 - - + +
252C ALA* 3.2 38.8 - - + +
262C ASN* 3.0 31.2 - - + +
263C ASP 4.4 2.0 - - - +
264C PRO* 4.7 1.3 - - + -
267C ASN* 3.3 35.2 - - + +
326C LEU* 3.3 26.1 + - + +
328C THR* 3.5 14.6 - - - +
329C GLY* 1.3 77.7 - - - +
331C HIS* 1.3 67.5 + - - +
332C VAL* 3.2 19.8 - - + +
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Residues in contact with HIS 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C TYR* 4.1 15.0 - - + -
250C VAL 3.2 7.8 + - - +
251C GLU* 3.1 29.2 + - + +
252C ALA 3.1 23.2 + - - -
320C VAL* 4.1 30.0 - - + +
321C LYS 4.5 4.0 + - - -
323C GLY* 3.4 24.0 + - - -
324C ILE 3.5 10.5 - - - -
325C LEU* 4.4 13.0 - - + +
330C LEU* 1.3 74.8 - - - +
332C VAL* 1.3 61.1 + - - +
333C HIS* 3.4 37.0 - + + -
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Residues in contact with VAL 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C GLU* 4.2 0.7 - - - -
252C ALA* 3.7 16.2 - - + -
264C PRO* 4.5 13.2 - - + -
324C ILE* 3.1 29.5 + - + +
326C LEU* 3.4 26.0 - - + -
330C LEU* 3.2 19.5 - - + +
331C HIS* 1.3 79.5 - - - +
333C HIS* 1.3 70.2 + - - +
336C SER* 3.5 30.5 - - - -
337C ALA* 4.5 4.3 - - + +
346C PHE* 3.4 8.7 - - + -
1002C F15 6.2 1.8 - - + -
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Residues in contact with HIS 333 (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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251C GLU* 3.9 15.0 + - - +
321C LYS 4.7 2.7 - - - -
322C ASP* 3.5 31.9 + - + +
331C HIS* 3.4 24.0 + + + -
332C VAL* 1.3 79.3 - - - +
334C ARG* 1.3 74.6 + - + +
335C ASN* 2.9 41.9 + - + +
336C SER* 3.3 18.3 + - - +
337C ALA* 3.5 7.4 + - - +
346C PHE* 3.7 4.4 - - - -
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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