Contacts of the helix formed by residues 2378 - 2385 (chain B) in PDB entry 1CVU
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 ALA2378 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2148B TYR* 4.2 0.4 - - - -
2149B THR* 3.2 19.7 - - + +
2151B ALA 4.7 2.5 - - - +
2376B ARG 3.4 2.4 + - - +
2377B ILE* 1.3 81.2 - - - +
2379B SER* 1.3 66.3 + - - +
2380B GLU* 3.8 10.5 - - - +
2381B PHE* 3.0 19.0 + - + +
2382B ASN* 3.3 7.8 + - - +
2529B PHE* 3.4 38.7 - - + -
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Residues in contact with SER2379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2148B TYR* 3.6 24.4 - - - +
2149B THR 2.7 16.4 + - - -
2150B ARG* 3.8 16.6 - - - -
2218B PRO 4.9 1.9 + - - -
2219B GLY* 5.4 1.8 - - - -
2378B ALA* 1.3 71.2 - - - +
2380B GLU* 1.3 57.3 + - - +
2382B ASN* 3.0 10.1 + - - +
2383B THR* 3.0 22.9 + - - -
2458B MET* 3.6 22.3 - - - +
2460B TYR* 2.6 27.6 + - - -
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Residues in contact with GLU2380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2150B ARG* 3.1 23.4 - - - -
2151B ALA* 2.8 34.2 + - - +
2152B LEU 3.2 2.9 + - - -
2378B ALA* 3.8 2.8 - - - +
2379B SER* 1.3 77.2 + - - +
2381B PHE* 1.3 63.1 + - - +
2383B THR* 3.7 3.6 - - - -
2384B LEU* 3.0 30.5 + - + +
2460B TYR* 3.4 17.0 - - + -
2466B TYR* 2.4 51.2 + - + +
2503B LEU* 4.7 7.4 - - + +
2525B LEU* 5.6 2.5 - - + -
2529B PHE* 4.2 14.6 - - + -
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Residues in contact with PHE2381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2209B PHE* 3.8 23.3 - + - -
2210B PHE* 3.4 17.7 - + + -
2377B ILE* 4.9 9.0 - - + -
2378B ALA* 3.0 19.7 + - + +
2380B GLU* 1.3 78.1 - - - +
2382B ASN* 1.3 63.6 + - - +
2384B LEU* 3.5 10.9 - - + +
2385B TYR* 3.2 52.1 + + - +
2526B GLY* 3.8 11.0 - - - -
2529B PHE* 3.4 47.9 - + + -
2530B SER* 4.0 16.4 - - - -
2533B GLY* 6.3 0.9 - - - -
2701B ACD 3.9 18.4 - - + -
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Residues in contact with ASN2382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2148B TYR* 3.3 30.9 + - + -
2210B PHE* 3.6 25.2 - - + +
2212B THR* 3.4 14.3 + - - -
2218B PRO 5.2 1.2 + - - -
2378B ALA 3.3 5.4 + - - +
2379B SER* 3.0 14.0 + - - +
2381B PHE* 1.3 82.1 - - - +
2383B THR* 1.3 63.3 + - - +
2385B TYR* 3.3 12.6 + - - +
2386B HIS* 3.2 12.9 + - - -
2704B BOG 3.2 36.9 + - - +
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Residues in contact with THR2383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2379B SER* 3.0 4.4 + - - -
2380B GLU 3.7 7.0 - - - -
2381B PHE 3.3 0.2 - - - -
2382B ASN* 1.3 76.6 - - - +
2384B LEU* 1.3 65.3 + - - +
2386B HIS* 2.9 35.1 + - + +
2451B SER* 5.3 0.7 - - - +
2455B SER* 4.1 13.9 + - - +
2458B MET* 4.5 5.9 - - - +
2460B TYR* 2.8 38.6 + - + -
2503B LEU* 4.8 7.2 - - + -
2504B TYR* 3.8 35.1 - - + +
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Residues in contact with LEU2384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2380B GLU 3.0 21.5 + - - +
2381B PHE* 3.5 21.8 - - + +
2383B THR* 1.3 77.0 - - - +
2385B TYR* 1.3 64.6 + - + +
2386B HIS 3.1 2.4 + - - +
2387B TRP* 2.8 25.0 + - - +
2503B LEU* 5.8 2.7 - - + +
2504B TYR* 5.7 1.3 - - - -
2507B LEU* 3.6 29.3 - - + +
2508B LEU* 6.0 0.2 - - - +
2522B MET* 3.3 25.2 - - - +
2525B LEU* 4.0 14.4 - - + -
2526B GLY* 3.9 24.5 - - - +
2529B PHE* 3.9 8.5 - - + -
2701B ACD 4.2 22.7 - - + -
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Residues in contact with TYR2385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2202B ALA* 4.5 5.8 - - + -
2206B THR* 3.4 26.3 - - + +
2210B PHE* 3.6 22.0 - + + -
2348B TYR* 2.5 28.8 + - - -
2381B PHE* 3.2 39.1 + + - +
2382B ASN 3.3 6.0 + - - +
2383B THR 3.0 1.2 - - - -
2384B LEU* 1.3 77.1 - - + +
2386B HIS* 1.3 50.0 + - - +
2387B TRP* 2.7 54.0 + + - +
2701B ACD 2.6 43.7 + - + +
2704B BOG 2.9 33.3 - - + +
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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