Contacts of the helix formed by residues 2549 - 2558 (chain B) 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 LEU2549 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2548B ALA* 1.3 88.9 - - + +
2550B ALA* 1.3 62.6 + - - +
2551B LEU 3.4 0.7 - - - -
2552B ASN* 3.5 16.9 + - + +
2553B ARG* 3.3 23.6 + - - +
2595B SER* 3.7 34.8 - - - +
2596B LEU* 4.7 3.8 - - - -
2597B THR* 5.7 1.6 - - - +
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Residues in contact with ALA2550 (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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2496B VAL* 4.6 9.6 - - + -
2497B PRO* 3.9 24.3 - - + +
2498B ASP* 5.9 1.8 - - - +
2548B ALA 3.2 8.7 - - - +
2549B LEU* 1.3 78.6 - - - +
2551B LEU* 1.3 62.8 + - - +
2553B ARG* 3.6 3.9 + - - +
2554B TYR* 3.2 23.0 + - - +
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Residues in contact with LEU2551 (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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2475B LEU* 6.3 2.9 - - + -
2478B PRO* 6.0 6.3 - - + -
2497B PRO* 4.0 15.8 - - + +
2548B ALA 4.0 8.5 + - - +
2549B LEU 3.4 0.4 - - - -
2550B ALA* 1.3 77.1 - - - +
2552B ASN* 1.3 64.9 + - - +
2554B TYR* 3.5 15.2 + - + +
2555B LEU* 3.7 11.3 + - - +
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Residues in contact with ASN2552 (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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2548B ALA 4.5 3.0 + - - +
2549B LEU* 3.5 23.7 + - + +
2550B ALA 3.3 0.6 - - - -
2551B LEU* 1.3 80.4 - - - +
2553B ARG* 1.3 64.9 + - - +
2554B TYR 3.4 0.5 + - - -
2555B LEU* 3.5 11.8 + - - +
2556B CYS* 3.8 10.4 + - - +
2590B LEU* 5.1 12.3 + - - +
2595B SER 3.5 13.9 + - - +
2596B LEU* 3.4 34.2 - - - +
2597B THR* 4.1 4.7 + - - -
2600B GLN* 5.0 6.2 - - - +
2604B ILE* 5.0 11.7 - - - +
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Residues in contact with ARG2553 (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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2549B LEU 3.3 14.1 + - - +
2550B ALA* 4.3 3.6 - - - +
2552B ASN* 1.3 80.8 + - - +
2554B TYR* 1.3 62.8 + - - +
2555B LEU 3.3 0.2 - - - -
2556B CYS* 3.7 6.4 + - - +
2557B LEU* 3.2 25.5 + - - +
2597B THR* 6.0 2.2 - - - +
2600B GLN* 5.8 3.4 - - - -
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Residues in contact with TYR2554 (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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2475B LEU* 6.1 4.3 - - + -
2497B PRO* 3.5 33.7 - - + +
2500B LYS* 3.3 33.9 - - + +
2501B ALA* 3.4 33.0 - - + -
2504B VAL* 3.9 2.9 - - + +
2527B PHE* 3.3 27.9 - + - -
2550B ALA 3.2 17.6 + - - +
2551B LEU* 3.7 10.5 - - + +
2552B ASN 3.2 0.8 - - - -
2553B ARG* 1.3 78.1 - - - +
2555B LEU* 1.3 67.2 + - + +
2557B LEU* 3.4 14.7 + - - +
2558B ALA 3.8 1.9 + - - -
2559B VAL* 3.5 27.2 - - + +
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Residues in contact with LEU2555 (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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2551B LEU 3.7 6.4 + - - +
2552B ASN* 3.5 9.3 + - - +
2553B ARG 3.3 0.4 - - - -
2554B TYR* 1.3 84.8 - - + +
2556B CYS* 1.3 59.8 + - - +
2557B LEU 3.2 0.2 - - - -
2559B VAL* 3.3 18.8 + - + -
2560B LEU* 2.9 43.9 + - + +
2590B LEU* 5.1 14.8 - - + -
2604B ILE* 6.1 2.9 - - + -
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Residues in contact with CYS2556 (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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2552B ASN 3.8 7.8 + - - +
2553B ARG* 3.7 6.8 + - - +
2555B LEU* 1.3 76.8 - - - +
2557B LEU* 1.3 63.5 + - - +
2560B LEU* 3.8 13.6 - - + +
2561B PRO* 4.0 4.1 - - - +
2600B GLN* 3.9 31.4 - - + +
2603B VAL* 3.6 32.7 - - + +
2604B ILE* 4.9 3.4 - - + -
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Residues in contact with LEU2557 (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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2501B ALA* 5.3 10.3 - - + -
2553B ARG 3.2 18.6 + - - +
2554B TYR* 3.6 9.6 - - - +
2555B LEU 3.2 0.6 - - - -
2556B CYS* 1.3 81.4 - - - +
2558B ALA* 1.3 64.2 + - + +
2561B PRO* 3.5 10.3 - - - +
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Residues in contact with ALA2558 (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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2501B ALA* 4.9 2.7 - - + +
2504B VAL* 3.7 25.5 - - + +
2505B LEU* 3.8 28.0 - - + +
2554B TYR 3.8 1.8 + - - -
2557B LEU* 1.3 81.4 - - + +
2559B VAL* 1.3 66.4 + - - +
2561B PRO* 3.5 10.7 - - - +
2562B LEU* 3.1 24.6 + - - +
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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