Contacts of the strand formed by residues 340 - 344 (chain C) in PDB entry 4BVH
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 ARG 340 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C VAL* 6.2 0.2 - - - -
315C LEU* 3.4 17.3 - - + +
317C ILE* 4.5 4.9 - - + -
331C THR* 2.8 33.7 + - - -
332C GLU* 2.8 20.4 + - - -
334C VAL* 3.9 16.8 - - + -
338C VAL 3.5 9.8 + - - +
339C PRO* 1.3 77.5 - - - +
341C LEU* 1.3 60.8 + - - +
342C LEU 4.0 0.4 - - - -
350C PRO 4.0 7.5 + - - -
351C LEU* 4.0 22.1 - - + +
354C HIS 3.1 23.2 + - - -
356C ARG* 3.6 25.7 - - - +
358C ARG 3.4 5.3 + - - +
359C ASP* 2.8 39.3 + - - +
360C VAL* 2.9 27.3 + - - +
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Residues in contact with LEU 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C LEU* 3.8 26.9 - - + -
128C VAL* 4.1 25.6 - - + -
314C LEU* 5.0 1.3 - - + -
315C LEU 2.9 9.5 + - - +
316C LEU* 3.4 20.9 - - + +
317C ILE* 2.8 34.5 + - - +
339C PRO 4.2 0.8 - - - -
340C ARG* 1.3 72.6 - - - +
342C LEU* 1.3 63.7 + - - +
343C ILE* 3.9 17.6 - - + +
360C VAL* 3.3 32.3 - - + +
362C GLN 4.3 3.4 - - - +
373C LEU* 3.9 22.4 - - + -
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Residues in contact with LEU 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C ILE* 3.4 36.6 - - + +
318C LEU* 5.3 0.7 - - - -
320C THR 4.9 1.1 - - - +
322C LEU* 5.2 1.8 - - + -
340C ARG 4.0 1.0 - - - -
341C LEU* 1.3 72.1 - - - +
343C ILE* 1.3 60.8 + - - +
344C ASN* 3.7 21.8 - - + +
346C ASP 3.5 22.2 - - - +
347C LEU* 3.8 26.2 - - + -
348C VAL* 3.9 20.2 - - + +
351C LEU* 4.3 19.0 - - + +
360C VAL 2.9 13.3 + - - +
361C ALA* 4.4 2.9 - - + -
362C GLN* 2.7 33.1 + - - +
363C LEU* 4.2 5.8 - - + -
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Residues in contact with ILE 343 (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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125C LEU* 5.4 0.7 - - + -
212C PHE* 6.0 0.7 - - + -
316C LEU* 6.0 2.7 - - + -
317C ILE 2.9 12.5 + - - +
318C LEU* 3.4 24.2 - - + -
319C GLY 3.1 23.0 + - - -
341C LEU* 3.9 27.6 - - + +
342C LEU* 1.3 77.5 - - - +
344C ASN* 1.3 62.6 + - - +
362C GLN* 3.5 15.9 - - + +
365C ASP 4.6 1.1 - - - +
366C VAL* 4.0 27.0 - - + +
369C GLY* 3.9 33.4 - - - +
370C VAL* 4.2 9.9 - - + -
373C LEU* 4.4 12.3 - - + -
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Residues in contact with ASN 344 (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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319C GLY* 3.2 25.7 - - - +
320C THR 3.3 17.2 + - - -
342C LEU* 3.7 16.9 - - + +
343C ILE* 1.3 76.6 - - - +
345C ARG* 1.3 71.0 - - - +
346C ASP 3.0 28.1 + - - +
348C VAL* 4.0 6.7 - - - +
362C GLN 3.4 4.6 + - - -
363C LEU* 3.2 9.4 - - - +
364C GLY 3.0 21.6 + - - -
1395C OAD 3.1 38.4 + - - -
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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
------------------------------------------------------------
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