Contacts of the helix formed by residues 2558 - 2566 (chain H) 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 ALA2558 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2501H ALA* 5.6 1.8 - - + -
2504H VAL* 3.7 27.3 - - + +
2505H LEU* 3.8 26.7 - - + -
2508H ASP* 6.6 0.2 - - + -
2554H TYR 3.8 1.8 + - - -
2557H LEU* 1.3 81.6 - - + +
2559H VAL* 1.3 65.4 + - - +
2561H PRO* 3.5 9.5 - - - +
2562H LEU* 3.1 23.7 + - - +
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Residues in contact with VAL2559 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2504H VAL* 4.7 5.4 - - + -
2527H PHE* 4.0 29.6 - - + -
2554H TYR* 3.5 52.0 - - + +
2555H LEU* 3.3 15.1 + - + +
2558H ALA* 1.3 77.1 - - - +
2560H LEU* 1.3 68.3 + - + +
2562H LEU* 3.2 21.9 + - + +
2563H ILE* 3.3 8.3 + - - +
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Residues in contact with LEU2560 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2555H LEU* 2.9 22.8 + - + +
2556H CYS* 3.8 12.1 - - - +
2559H VAL* 1.3 78.5 - - + +
2561H PRO* 1.3 71.5 - - + +
2563H ILE* 3.1 15.9 + - + +
2564H THR* 3.3 16.1 + - - +
2587H VAL* 6.0 4.5 - - + -
2603H VAL* 3.7 22.0 - - + +
2604H ILE* 3.7 43.3 - - + -
2607H CYS* 3.7 27.9 - - + +
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Residues in contact with PRO2561 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2556H CYS 4.0 11.7 - - - +
2557H LEU 3.5 19.5 - - - +
2558H ALA* 3.5 17.3 - - - +
2560H LEU* 1.3 94.5 - - + +
2562H LEU* 1.3 58.1 + - - +
2564H THR* 2.6 22.5 + - + +
2565H LYS* 3.3 12.0 + - - +
2603H VAL* 4.3 8.0 - - + -
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Residues in contact with LEU2562 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2504H VAL* 5.2 8.5 - - + +
2507H LEU* 4.4 20.9 - - + -
2508H ASP* 4.1 26.7 - - + -
2512H GLY* 5.9 3.4 - - - -
2527H PHE* 4.8 22.0 - - + -
2558H ALA 3.1 21.5 + - - +
2559H VAL* 3.3 8.1 - - + +
2560H LEU 3.1 1.2 - - - -
2561H PRO* 1.3 76.7 - - - +
2563H ILE* 1.3 63.6 + - - +
2565H LYS* 3.4 8.8 + - + +
2566H CYS* 3.2 24.4 + - + +
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Residues in contact with ILE2563 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2559H VAL 3.3 7.2 + - - +
2560H LEU* 3.1 11.4 + - + +
2562H LEU* 1.3 76.5 - - - +
2564H THR* 1.3 65.6 + - - +
2566H CYS* 3.3 14.8 + - - +
2567H ALA* 3.4 12.5 + - - +
2570H PHE* 6.2 1.7 - - + -
2607H CYS* 4.4 18.8 - - - -
2611H LEU* 4.4 15.5 - - + +
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Residues in contact with THR2564 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2560H LEU 3.3 10.6 + - - +
2561H PRO* 2.6 31.2 + - + +
2563H ILE* 1.3 77.1 - - - +
2565H LYS* 1.3 58.3 + - - -
2567H ALA* 3.4 17.1 + - - +
2568H PRO* 5.0 0.5 - - - +
2606H GLU* 4.0 17.7 - - + +
2607H CYS* 4.5 7.2 - - - +
2610H ALA* 3.7 30.1 - - + +
2611H LEU* 5.7 0.4 - - + -
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Residues in contact with LYS2565 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2561H PRO 3.3 9.5 + - - +
2562H LEU* 3.8 14.1 - - + +
2563H ILE 3.3 0.2 - - - -
2564H THR* 1.3 81.2 + - - +
2566H CYS* 1.3 57.2 + - - +
2567H ALA 3.3 3.4 + - - -
2568H PRO* 4.0 9.9 - - - +
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Residues in contact with CYS2566 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2562H LEU* 3.2 19.3 + - + +
2563H ILE* 3.3 9.0 + - - +
2564H THR 3.3 0.4 - - - -
2565H LYS* 1.3 75.7 - - - +
2567H ALA* 1.3 63.0 + - - +
2568H PRO* 3.5 2.9 - - - -
2569H LEU* 3.4 16.6 + - + -
2570H PHE* 3.1 24.9 + - + +
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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