Contacts of the helix formed by residues 2463 - 2472 (chain F) in PDB entry 6X34
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 PRO2463 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2459F ARG 3.8 2.9 - - - +
2460F SER* 4.3 10.3 - - - +
2461F LEU 3.3 11.4 - - - +
2462F VAL* 1.3 92.7 - - + +
2464F LEU* 1.3 66.5 + - - +
2465F ASP* 3.1 12.8 + - + +
2466F ASP* 3.4 17.0 + - + +
2467F LEU* 3.6 8.5 + - - +
2506F PHE* 5.2 0.3 - - - -
2511F TYR* 3.8 14.8 - - - +
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Residues in contact with LEU2464 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2463F PRO* 1.3 72.4 - - - +
2465F ASP* 1.3 59.1 + - - +
2467F LEU* 3.3 15.2 + - + +
2468F VAL* 2.9 31.9 + - - +
2507F LEU* 4.6 15.9 - - + -
2511F TYR* 3.6 54.1 + - + -
2519F LEU* 5.4 14.8 - - + -
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Residues in contact with ASP2465 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2378F LEU* 4.9 2.9 - - - +
2463F PRO* 3.1 10.3 - - + +
2464F LEU* 1.3 77.7 - - - +
2466F ASP* 1.3 57.5 + - - +
2468F VAL* 3.1 12.3 - - + +
2469F GLY* 2.9 25.8 + - - -
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Residues in contact with ASP2466 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2377F LEU* 3.7 28.6 - - + +
2378F LEU* 4.8 11.7 - - - +
2462F VAL* 3.6 25.8 - - + -
2463F PRO* 3.4 11.2 + - + +
2464F LEU 3.4 0.4 - - - -
2465F ASP* 1.3 77.4 - - - +
2467F LEU* 1.3 57.8 + - - +
2469F GLY* 3.4 2.0 + - - +
2470F ILE* 2.9 31.0 + - - +
2503F MET* 5.4 0.8 - - - +
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Residues in contact with LEU2467 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2462F VAL* 4.9 1.3 - - - +
2463F PRO 3.6 5.6 + - - +
2464F LEU* 3.3 19.2 + - + +
2465F ASP 3.2 0.4 - - - -
2466F ASP* 1.3 78.9 - - - +
2468F VAL* 1.3 57.2 + - - +
2470F ILE* 3.3 6.0 + - - +
2471F ILE* 2.9 33.7 + - + +
2503F MET* 5.2 9.9 - - + +
2506F PHE* 4.8 20.9 - - + -
2507F LEU* 4.4 22.2 - - + -
2511F TYR* 6.0 0.2 - - + -
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Residues in contact with VAL2468 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2464F LEU* 2.9 18.8 + - + +
2465F ASP* 3.1 21.5 - - - +
2467F LEU* 1.3 75.9 - - - +
2469F GLY* 1.3 58.6 + - - +
2471F ILE* 3.4 10.1 + - + +
2472F SER* 2.9 30.3 + - - -
2507F LEU* 5.5 3.3 - - + +
2519F LEU* 6.0 7.0 - - + -
2522F VAL* 3.7 29.6 - - + +
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Residues in contact with GLY2469 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2378F LEU* 3.5 30.0 - - - +
2465F ASP 2.9 14.2 + - - -
2466F ASP 3.8 0.7 - - - -
2468F VAL* 1.3 80.0 - - - +
2470F ILE* 1.3 60.6 + - - +
2472F SER* 3.4 12.7 + - - -
2473F LEU* 3.4 20.8 + - - +
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Residues in contact with ILE2470 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2377F LEU* 6.0 3.6 - - + -
2378F LEU* 3.8 5.5 - - + +
2381F ILE* 5.7 4.3 - - + -
2466F ASP 2.9 17.2 + - - +
2467F LEU 3.8 2.9 - - - +
2469F GLY* 1.3 73.3 - - - +
2471F ILE* 1.3 66.0 + - - +
2473F LEU* 3.4 32.6 + - + +
2495F PHE* 5.9 1.6 - - - -
2500F LYS* 4.6 5.4 - - - +
2503F MET* 3.8 38.2 - - + +
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Residues in contact with ILE2471 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2467F LEU* 2.9 23.2 + - + +
2468F VAL* 3.7 10.3 - - + +
2469F GLY 3.3 0.2 - - - -
2470F ILE* 1.3 77.3 - - - +
2472F SER* 1.3 57.5 + - - +
2473F LEU 3.1 5.5 + - - -
2500F LYS* 3.3 34.1 + - + +
2503F MET* 3.8 20.9 - - + -
2504F VAL* 3.7 31.2 - - + +
2507F LEU* 4.9 13.5 - - + -
2522F VAL 5.8 0.2 - - - +
2523F LEU* 6.2 1.1 - - - -
2526F GLY* 4.0 29.2 - - - +
2527F PHE* 4.4 20.0 - - + -
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Residues in contact with SER2472 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2468F VAL* 2.9 21.3 + - - -
2469F GLY* 3.8 8.7 - - - -
2470F ILE 3.3 0.8 - - - -
2471F ILE* 1.3 73.8 - - - +
2473F LEU* 1.3 62.8 + - - +
2474F PRO* 3.6 5.0 - - - +
2526F GLY* 5.0 11.0 - - - -
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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