Contacts of the helix formed by residues 2552 - 2561 (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 GLY2552 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A MET* 3.6 16.9 - - - -
2547B PRO* 3.0 24.0 + - - +
2548B SER 4.5 0.4 - - - -
2550B PHE 4.0 0.2 - - - +
2551B GLY* 1.3 81.2 - - - +
2553B GLU* 1.3 61.6 + - - -
2554B VAL 3.2 3.9 + - - -
2555B GLY* 3.3 2.3 + - - -
2556B PHE* 2.9 28.2 + - - +
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Residues in contact with GLU2553 (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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56A LYS* 5.6 7.6 - - - +
2547B PRO* 2.8 43.0 - - + +
2552B GLY* 1.3 72.2 - - - -
2554B VAL* 1.3 59.4 + - + +
2556B PHE* 3.6 10.8 - - - +
2557B LYS* 2.9 30.1 + - - +
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Residues in contact with VAL2554 (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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2315B ILE* 3.6 30.5 - - + -
2316B LEU* 5.7 1.1 - - + -
2319B GLU* 3.4 38.8 - - + +
2551B GLY 5.5 2.5 - - - +
2552B GLY 3.2 0.8 - - - -
2553B GLU* 1.3 77.6 - - + +
2555B GLY* 1.3 64.4 + - - +
2557B LYS* 3.0 18.2 + - - +
2558B ILE* 3.2 14.3 + - + +
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Residues in contact with GLY2555 (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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2316B LEU* 4.7 6.8 - - - +
2335B ILE* 3.6 20.4 - - - +
2550B PHE* 3.4 23.3 + - - -
2551B GLY 5.0 0.4 - - - -
2552B GLY* 3.3 4.9 + - - -
2554B VAL* 1.3 79.8 - - - +
2556B PHE* 1.3 60.7 + - - +
2558B ILE* 3.2 24.7 + - - +
2559B ILE* 3.5 8.1 + - - +
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Residues in contact with PHE2556 (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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2545B TRP* 3.6 48.2 - + - -
2546B LYS* 4.4 4.3 - - - -
2547B PRO* 3.9 24.0 - - + -
2550B PHE* 3.3 40.2 - + + +
2552B GLY 2.9 17.5 + - - +
2553B GLU* 3.6 26.2 - - - +
2555B GLY* 1.3 76.5 - - - +
2557B LYS* 1.3 61.1 + - - +
2559B ILE* 3.3 8.7 + - + +
2560B ASN* 2.9 40.7 + - - -
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Residues in contact with LYS2557 (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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2553B GLU 2.9 14.1 + - - +
2554B VAL* 3.0 11.2 + - - +
2556B PHE* 1.3 74.9 - - - +
2558B ILE* 1.3 64.3 + - - +
2560B ASN* 4.3 5.8 - - + +
2561B THR* 2.7 53.7 + - + +
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Residues in contact with ILE2558 (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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2308B GLU* 4.3 4.7 - - - +
2311B ARG* 4.6 13.0 - - - +
2312B VAL* 4.2 20.0 - - + -
2315B ILE* 4.1 34.1 - - + -
2316B LEU* 5.8 0.4 - - + -
2335B ILE* 3.5 9.6 - - + -
2339B GLU* 3.3 30.9 - - - +
2554B VAL* 3.2 8.9 + - + +
2555B GLY* 3.4 23.6 - - - +
2557B LYS* 1.3 80.2 - - - +
2559B ILE* 1.3 60.9 + - - +
2561B THR* 3.8 4.2 + - - -
2562B ALA* 3.2 22.2 + - - +
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Residues in contact with ILE2559 (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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2335B ILE* 3.6 24.7 - - + +
2338B GLY* 3.7 31.9 - - - +
2339B GLU* 4.2 6.7 - - - -
2342B LYS* 3.4 22.5 - - - +
2361B PHE* 4.1 7.0 - - + -
2545B TRP* 4.0 22.7 - - + -
2550B PHE* 3.5 49.8 - - + -
2555B GLY 3.5 8.9 + - - +
2556B PHE* 3.3 7.4 + - + +
2557B LYS 3.1 0.2 - - - -
2558B ILE* 1.3 80.2 - - - +
2560B ASN* 1.3 62.4 + - - +
2561B THR 3.3 1.0 + - - -
2562B ALA* 3.4 2.8 + - - +
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Residues in contact with ASN2560 (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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2342B LYS* 2.9 25.4 + - - +
2361B PHE* 4.9 8.7 - - - +
2545B TRP* 3.5 23.2 - - - -
2556B PHE* 2.9 55.1 + - - +
2557B LYS* 3.2 6.9 + - + +
2559B ILE* 1.3 76.6 - - - +
2561B THR* 1.3 64.3 + - + +
2562B ALA 3.5 0.4 - - - -
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Residues in contact with THR2561 (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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2342B LYS* 4.5 1.6 - - - +
2557B LYS* 2.7 50.3 + - + +
2558B ILE* 3.8 4.7 + - - -
2560B ASN* 1.3 82.2 - - + +
2562B ALA* 1.3 65.8 + - - +
2563B SER* 3.6 3.8 + - - -
2566B SER* 4.1 10.7 + - - -
2596F LYS* 4.3 17.0 + - - +
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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