Contacts of the helix formed by residues 2563 - 2572 (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 SER2563 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2343B ILE* 3.6 8.5 - - - +
2347B ASP* 3.1 17.9 - - - -
2561B THR 3.6 3.7 + - - -
2562B ALA* 1.3 77.7 - - - +
2564B ILE* 1.3 64.0 + - - +
2565B GLN* 3.4 9.2 + - - +
2566B SER* 3.0 30.6 + - - -
2567B LEU* 3.0 23.9 + - - +
2595F THR 5.6 1.9 + - - -
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Residues in contact with ILE2564 (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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2197B MET* 5.3 2.5 - - + -
2201B PHE* 4.0 17.5 - - + -
2301B TYR* 4.4 6.5 - - + +
2343B ILE* 3.8 7.9 - - + +
2347B ASP* 2.8 30.2 + - + +
2563B SER* 1.3 72.5 - - - +
2565B GLN* 1.3 65.4 + - + +
2567B LEU* 3.8 14.3 - - + +
2568B ILE* 3.3 42.2 + - + +
2578B THR* 3.7 8.9 - - + +
2579B SER* 4.4 21.1 - - - -
2580B PHE* 3.8 38.1 - - + +
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Residues in contact with GLN2565 (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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2563B SER* 3.1 8.3 + - - +
2564B ILE* 1.3 81.5 - - + +
2566B SER* 1.3 54.9 + - - +
2568B ILE 3.4 0.3 + - - -
2569B CYS* 2.7 44.2 + - + +
2575B CYS* 4.4 2.0 - - - -
2576B PRO 3.0 23.0 + - - -
2577B PHE* 3.3 22.7 - - + -
2578B THR* 2.9 37.4 + - - +
2595F THR* 4.7 13.7 - - - +
2598F ALA* 4.2 21.2 - - + +
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Residues in contact with SER2566 (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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2561B THR 4.1 6.8 + - - -
2562B ALA* 5.0 2.7 - - - -
2563B SER* 3.0 26.4 + - - -
2565B GLN* 1.3 74.2 - - - +
2567B LEU* 1.3 61.8 + - - +
2569B CYS* 4.1 5.4 - - - -
2570B ASN* 2.8 49.9 + - - +
2595F THR 5.4 3.3 + - - -
2596F LYS* 4.0 18.5 + - - -
2597F THR* 4.9 10.4 + - - -
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Residues in contact with LEU2567 (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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2201B PHE* 5.1 0.7 - - + -
2301B TYR* 5.1 4.0 - - + -
2304B ILE* 3.7 19.4 - - + +
2305B TRP* 3.8 53.6 - - + +
2308B GLU* 3.9 28.7 - - + -
2339B GLU* 4.7 5.8 - - - +
2343B ILE* 4.4 7.0 - - + -
2563B SER 3.0 15.5 + - - +
2564B ILE* 3.8 24.9 - - + +
2565B GLN 3.3 0.2 - - - -
2566B SER* 1.3 78.2 - - - +
2568B ILE* 1.3 64.6 + - + +
2570B ASN* 5.0 0.9 - - - +
2571B ASN* 2.8 32.0 + - - +
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Residues in contact with ILE2568 (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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2197B MET* 4.0 25.6 - - + -
2301B TYR* 4.7 1.6 - - + -
2304B ILE* 4.2 13.9 - - + -
2423B VAL* 4.1 11.4 - - + -
2564B ILE* 3.3 38.4 + - + +
2565B GLN* 3.9 3.1 - - - +
2566B SER 3.2 0.4 - - - -
2567B LEU* 1.3 89.7 - - + +
2569B CYS* 1.3 61.1 + - - +
2572B VAL* 2.7 58.1 + - + +
2576B PRO* 3.6 32.1 - - + +
2578B THR* 4.0 5.8 - - + -
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Residues in contact with CYS2569 (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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2565B GLN* 2.7 28.0 + - + +
2566B SER* 3.7 5.8 - - - +
2568B ILE* 1.3 76.7 - - - +
2570B ASN* 1.3 61.2 + - - +
2571B ASN 3.4 0.2 + - - -
2572B VAL 3.7 11.1 - - - +
2575B CYS* 2.0 57.8 + - - +
2597F THR* 3.5 11.2 - - + -
2598F ALA* 3.8 3.1 - - - +
2601F ASN* 3.3 29.9 + - - +
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Residues in contact with ASN2570 (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* 4.8 0.6 + - - -
2311B ARG* 3.7 48.6 + - - +
2566B SER* 2.8 35.9 + - - +
2567B LEU* 5.0 0.4 - - - +
2569B CYS* 1.3 73.9 - - - +
2571B ASN* 1.3 69.3 + - - +
2597F THR* 3.7 21.4 + - - +
2601F ASN* 4.5 2.5 + - - +
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Residues in contact with ASN2571 (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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2304B ILE* 3.9 13.7 + - + +
2307B ARG* 3.0 48.5 + - + +
2308B GLU* 3.0 56.2 + - - +
2311B ARG* 3.9 7.1 - - - +
2567B LEU* 2.8 27.1 + - - +
2568B ILE 3.0 2.6 + - - -
2570B ASN* 1.3 86.0 - - - +
2572B VAL* 1.3 63.1 + - + +
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Residues in contact with VAL2572 (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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2304B ILE* 4.1 24.7 - - + -
2307B ARG* 4.4 2.2 - - - +
2419B LEU* 3.8 13.0 - - + +
2420B THR* 3.6 36.1 - - - +
2423B VAL* 4.1 4.3 - - + -
2568B ILE* 2.7 37.1 + - + +
2569B CYS 3.7 4.7 - - - +
2570B ASN 3.8 0.4 - - - -
2571B ASN* 1.3 79.6 - - - +
2573B LYS* 1.3 70.1 + - - +
2574B GLY 3.2 0.3 + - - -
2575B CYS* 2.9 18.7 + - - -
2576B PRO* 3.7 17.3 - - + -
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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