Contacts of the helix formed by residues 2444 - 2458 (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 VAL2444 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2388B HIS* 3.9 31.0 - - + +
2391B LEU* 4.9 8.7 - - + -
2404B PHE* 4.6 17.9 - - + -
2440B VAL* 4.0 7.6 - - + -
2441B PRO* 2.9 21.6 + - + +
2443B ALA* 1.3 82.6 - - - +
2445B GLN* 1.3 62.9 + - - +
2446B ALA* 3.3 3.1 - - - -
2447B VAL* 3.1 40.1 + - + +
2448B ALA* 3.3 3.8 + - - +
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Residues in contact with GLN2445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2178B LEU* 3.7 16.8 - - + +
2179B GLU* 5.3 2.8 - - - +
2183B LEU* 3.6 37.8 - - + +
2440B VAL* 4.7 0.9 - - - -
2441B PRO 3.5 3.0 + - - -
2442B ILE* 3.1 30.7 + - - +
2443B ALA 3.6 0.6 - - - -
2444B VAL* 1.3 75.7 - - - +
2446B ALA* 1.3 64.9 + - + +
2448B ALA* 3.0 10.3 + - - +
2449B LYS* 2.9 28.6 + - - +
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Residues in contact with ALA2446 (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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2444B VAL 3.3 1.2 - - - -
2445B GLN* 1.3 84.1 - - + +
2447B VAL* 1.3 58.4 + - + +
2449B LYS* 3.3 8.4 + - - +
2450B ALA* 3.0 29.5 + - - +
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Residues in contact with VAL2447 (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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2386B HIS* 5.0 3.4 - - + +
2388B HIS* 3.2 40.6 - - + +
2444B VAL* 3.1 29.7 + - + +
2446B ALA* 1.3 81.4 - - + +
2448B ALA* 1.3 62.3 + - - +
2450B ALA* 3.3 7.5 + - + +
2451B SER* 3.2 22.7 + - - +
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Residues in contact with ALA2448 (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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2178B LEU* 4.1 14.8 - - + -
2182B LEU* 4.8 2.7 - - + -
2388B HIS* 5.1 2.7 - - + -
2440B VAL* 3.9 31.4 - - + -
2444B VAL 3.3 1.6 + - - -
2445B GLN 3.0 9.0 + - - +
2447B VAL* 1.3 82.2 - - - +
2449B LYS* 1.3 61.1 + - - +
2451B SER* 3.5 1.5 + - - -
2452B ILE* 3.4 24.1 + - - +
2504B TYR* 3.5 26.3 - - + +
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Residues in contact with LYS2449 (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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2173B ASP* 5.2 1.1 - - - -
2174B SER* 3.1 37.9 + - - +
2175B LYS* 4.2 19.7 - - + +
2178B LEU* 4.5 14.7 - - + +
2445B GLN 2.9 15.5 + - - +
2446B ALA* 3.7 8.5 - - - +
2447B VAL 3.2 0.2 - - - -
2448B ALA* 1.3 74.9 - - - +
2450B ALA* 1.3 56.1 + - - +
2452B ILE* 3.1 8.2 + - - +
2453B ASP* 2.8 54.9 + - - +
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Residues in contact with ALA2450 (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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2446B ALA 3.0 17.5 + - - +
2447B VAL* 3.5 8.5 - - + +
2449B LYS* 1.3 74.6 - - - +
2451B SER* 1.3 57.5 + - - +
2453B ASP* 4.2 7.4 - - - -
2454B GLN* 2.6 58.7 + - + +
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Residues in contact with SER2451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2383B THR* 5.6 0.9 - - - -
2386B HIS* 3.5 33.4 + - - +
2388B HIS* 5.0 0.2 + - - -
2447B VAL* 3.2 13.5 + - - +
2448B ALA* 3.6 1.7 - - - -
2449B LYS 3.3 0.2 - - - -
2450B ALA* 1.3 77.7 - - - +
2452B ILE* 1.3 57.1 + - - +
2454B GLN* 4.3 7.3 - - - +
2455B SER* 2.4 35.5 + - - -
2504B TYR* 3.3 39.5 + - - -
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Residues in contact with ILE2452 (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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2174B SER* 3.6 40.4 - - - +
2177B VAL* 4.4 11.2 - - + -
2178B LEU* 4.5 1.8 - - + +
2182B LEU* 4.0 22.7 - - + -
2448B ALA 3.4 14.1 - - - +
2449B LYS* 3.1 9.6 + - - +
2450B ALA 3.1 0.6 - - - -
2451B SER* 1.3 76.9 - - - +
2453B ASP* 1.3 67.1 + - - +
2455B SER* 3.3 4.4 + - - -
2456B ARG* 3.1 49.6 + - - +
2495B TYR* 5.5 0.4 - - - +
2502B GLU* 4.0 9.1 - - - +
2504B TYR* 3.8 16.6 - - + -
2505B PRO* 4.5 11.0 - - + -
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Residues in contact with ASP2453 (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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2174B SER* 2.7 26.9 + - - -
2449B LYS* 2.8 48.6 + - - +
2450B ALA* 3.8 6.5 - - - +
2452B ILE* 1.3 73.3 - - - +
2454B GLN* 1.3 59.1 + - + +
2456B ARG* 3.2 15.5 + - - +
2457B GLU* 3.0 33.3 + - + +
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Residues in contact with GLN2454 (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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2212B THR* 6.3 0.6 - - - +
2214B HIS* 5.4 7.3 + - - -
2218B PRO* 4.0 29.3 - - + +
2386B HIS* 5.6 0.8 + - - -
2450B ALA* 2.6 41.3 + - + +
2451B SER* 4.3 4.9 - - - +
2453B ASP* 1.3 72.1 - - + +
2455B SER* 1.3 64.4 + - - +
2457B GLU* 3.1 20.9 + - - +
2458B MET* 3.0 32.2 + - + +
2704B BOG 3.7 22.2 + - - -
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Residues in contact with SER2455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2383B THR* 4.1 21.1 + - - +
2451B SER 2.4 27.2 + - - -
2452B ILE* 3.6 6.4 - - - -
2454B GLN* 1.3 76.6 - - - +
2456B ARG* 1.3 62.9 + - - +
2458B MET* 3.4 12.5 + - - +
2459B LYS 3.3 4.0 + - - -
2460B TYR* 3.1 47.3 + - - +
2502B GLU* 5.4 3.8 - - - -
2504B TYR* 4.4 7.0 - - - +
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Residues in contact with ARG2456 (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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2171B LEU* 3.5 35.1 + - + +
2172B PRO 2.7 31.8 + - - -
2173B ASP* 4.8 0.4 - - - +
2174B SER* 3.6 24.2 + - - +
2177B VAL* 4.6 2.4 - - - +
2452B ILE* 3.1 24.9 + - - +
2453B ASP* 3.3 12.9 + - - +
2454B GLN 3.1 0.2 - - - -
2455B SER* 1.3 75.6 - - - +
2457B GLU* 1.3 66.1 + - - +
2459B LYS* 2.9 22.1 + - - +
2460B TYR 4.9 0.7 - - - +
2495B TYR* 4.0 4.2 + - - -
2502B GLU* 2.6 42.6 + - - +
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Residues in contact with GLU2457 (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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2132B VAL* 5.2 1.9 - - - +
2218B PRO* 3.8 21.0 - - + +
2453B ASP* 3.0 18.9 + - - +
2454B GLN* 3.1 27.0 + - - +
2456B ARG* 1.3 77.2 - - - +
2458B MET* 1.3 59.9 + - + +
2459B LYS* 3.0 15.4 + - - +
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Residues in contact with MET2458 (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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2132B VAL* 4.0 19.9 - - + +
2150B ARG* 2.6 46.9 + - - +
2154B PRO* 3.9 2.8 - - - +
2218B PRO* 3.6 26.5 - - + +
2219B GLY* 3.6 28.0 - - - +
2379B SER* 3.6 20.0 - - - +
2383B THR* 4.5 6.1 - - - +
2454B GLN* 3.0 28.5 + - + +
2455B SER* 4.0 3.1 - - - +
2456B ARG 3.3 0.2 - - - -
2457B GLU* 1.3 72.5 - - - +
2459B LYS* 1.3 57.3 + - - +
2460B TYR* 3.3 26.5 - - + +
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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