Contacts of the helix formed by residues 2549 - 2558 (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 LEU2549 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2548F ALA* 1.3 89.4 - - + +
2550F ALA* 1.3 62.4 + - - +
2551F LEU 3.4 0.7 - - - -
2552F ASN* 3.5 15.9 + - + +
2553F ARG* 3.3 23.4 + - - +
2595F SER* 3.7 33.9 - - - +
2596F LEU* 4.7 4.5 - - - +
2597F THR* 6.0 1.3 - - - +
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Residues in contact with ALA2550 (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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2496F VAL* 4.6 9.9 - - + -
2497F PRO* 3.9 24.6 - - + +
2498F ASP* 5.9 2.0 - - - +
2548F ALA 3.2 8.7 - - - +
2549F LEU* 1.3 79.3 - - - +
2551F LEU* 1.3 62.7 + - - +
2553F ARG* 3.6 3.3 + - - +
2554F TYR* 3.2 23.2 + - - +
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Residues in contact with LEU2551 (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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2475F LEU* 6.3 2.9 - - + -
2478F PRO* 6.0 6.1 - - + -
2497F PRO* 4.0 15.1 - - + +
2548F ALA 4.0 8.7 + - - +
2549F LEU 3.4 0.4 - - - -
2550F ALA* 1.3 76.6 - - - +
2552F ASN* 1.3 65.7 + - - +
2554F TYR* 3.5 15.7 + - + +
2555F LEU* 3.7 11.3 + - - +
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Residues in contact with ASN2552 (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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2548F ALA 4.5 3.0 + - - +
2549F LEU* 3.5 23.9 + - + +
2550F ALA 3.3 0.6 - - - -
2551F LEU* 1.3 81.4 - - - +
2553F ARG* 1.3 64.6 + - - +
2554F TYR 3.4 0.7 + - - -
2555F LEU* 3.5 11.0 + - - +
2556F CYS* 3.8 10.0 + - - +
2590F LEU* 5.1 12.1 + - - +
2595F SER 3.5 13.9 + - - +
2596F LEU* 3.4 33.2 - - - +
2597F THR* 4.1 5.4 + - - -
2600F GLN* 5.0 5.7 - - - +
2604F ILE* 5.0 12.7 - - - +
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Residues in contact with ARG2553 (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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2549F LEU 3.3 14.8 + - - +
2550F ALA* 4.3 3.1 - - - +
2552F ASN* 1.3 80.2 + - - +
2554F TYR* 1.3 62.9 + - - +
2556F CYS* 3.9 5.5 - - - +
2557F LEU* 3.2 24.6 + - - +
2597F THR* 6.0 2.2 - - - +
2600F GLN* 5.8 3.4 - - - -
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Residues in contact with TYR2554 (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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2475F LEU* 6.1 4.5 - - + -
2497F PRO* 3.5 32.3 - - + +
2500F LYS* 3.3 33.8 - - + +
2501F ALA* 3.4 33.7 - - + -
2504F VAL* 3.9 3.1 - - + +
2527F PHE* 3.3 27.7 - + - -
2550F ALA 3.2 18.7 + - - +
2551F LEU* 3.7 11.0 - - + +
2552F ASN 3.2 0.6 - - - -
2553F ARG* 1.3 76.7 - - - +
2555F LEU* 1.3 70.1 + - + +
2557F LEU* 3.4 14.9 + - - +
2558F ALA 3.8 1.6 + - - -
2559F VAL* 3.5 27.2 - - + +
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Residues in contact with LEU2555 (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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2551F LEU 3.7 6.8 + - - +
2552F ASN* 3.5 9.5 + - - +
2553F ARG 3.3 0.6 - - - -
2554F TYR* 1.3 83.1 - - + +
2556F CYS* 1.3 60.3 + - - +
2557F LEU 3.2 0.4 - - - -
2559F VAL* 3.3 18.7 + - + -
2560F LEU* 2.9 42.4 + - + +
2590F LEU* 5.1 15.5 - - + -
2604F ILE* 6.1 3.6 - - + -
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Residues in contact with CYS2556 (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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2552F ASN 3.8 7.0 + - - +
2553F ARG* 3.7 6.7 + - - +
2554F TYR 3.4 0.2 - - - -
2555F LEU* 1.3 76.6 - - - +
2557F LEU* 1.3 63.7 + - - +
2560F LEU* 3.8 13.6 - - + +
2561F PRO* 4.0 3.7 - - - +
2600F GLN* 3.9 31.2 - - + +
2603F VAL* 3.6 33.8 - - + +
2604F ILE* 4.9 4.0 - - + -
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Residues in contact with LEU2557 (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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2501F ALA* 5.3 9.6 - - + -
2553F ARG 3.2 18.6 + - - +
2554F TYR* 3.6 9.4 - - - +
2555F LEU 3.2 1.2 - - - -
2556F CYS* 1.3 80.6 - - - +
2558F ALA* 1.3 63.5 + - + +
2561F PRO* 3.5 11.2 - - - +
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Residues in contact with ALA2558 (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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2501F ALA* 4.9 2.9 - - + +
2504F VAL* 3.7 27.1 - - + +
2505F LEU* 3.8 27.1 - - + +
2508F ASP* 6.6 0.2 - - + -
2554F TYR 3.8 1.6 + - - -
2557F LEU* 1.3 80.6 - - + +
2559F VAL* 1.3 67.7 + - - +
2561F PRO* 3.5 10.4 - - - +
2562F LEU* 3.1 24.1 + - - +
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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