Contacts of the helix formed by residues 2597 - 2611 (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 THR2597 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2549F LEU* 5.7 1.6 - - - +
2552F ASN* 4.1 4.8 + - - -
2553F ARG* 6.0 2.4 - - - +
2596F LEU* 1.3 75.5 - - - +
2598F LYS* 1.3 56.4 + - + +
2599F ALA* 3.5 20.4 - - + +
2600F GLN* 3.1 20.3 + - + +
2601F ARG* 2.8 35.0 + - - +
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Residues in contact with LYS2598 (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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2596F LEU 3.7 3.2 + - - -
2597F THR* 1.3 74.3 - - + +
2599F ALA* 1.3 61.9 + - - +
2601F ARG* 3.4 18.9 + - - +
2602F ASP* 3.8 5.7 + - - +
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Residues in contact with ALA2599 (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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2597F THR* 3.2 12.5 - - + +
2598F LYS* 1.3 80.3 - - - +
2600F GLN* 1.3 59.9 + - - +
2601F ARG 3.5 0.5 + - - -
2602F ASP* 3.6 16.5 + - - +
2603F VAL* 4.1 8.5 + - - +
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Residues in contact with GLN2600 (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* 5.0 7.6 - - - +
2553F ARG* 5.8 5.2 - - + -
2556F CYS* 3.9 18.9 - - + +
2596F LEU* 5.6 1.3 - - + -
2597F THR* 3.1 25.4 + - + +
2599F ALA* 1.3 75.9 - - - +
2601F ARG* 1.3 63.7 + - - +
2602F ASP 3.3 0.4 - - - -
2603F VAL* 3.2 21.0 + - - +
2604F ILE* 3.4 17.4 + - + +
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Residues in contact with ARG2601 (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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2591F SER* 6.0 0.7 - - - +
2596F LEU* 5.6 6.1 - - + -
2597F THR 2.8 15.3 + - - +
2598F LYS* 3.5 12.8 - - - +
2599F ALA 3.2 0.6 - - - -
2600F GLN* 1.3 78.8 - - - +
2602F ASP* 1.3 60.8 + - - +
2604F ILE* 3.3 12.0 + - - +
2605F GLU* 3.1 21.3 + - - +
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Residues in contact with ASP2602 (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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2598F LYS 3.8 5.3 + - - +
2599F ALA* 3.6 12.1 + - - +
2600F GLN 3.3 0.6 - - - -
2601F ARG* 1.3 75.6 - - - +
2603F VAL* 1.3 60.7 + - + +
2605F GLU* 3.4 7.4 + - - +
2606F GLU* 2.8 30.7 + - - +
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Residues in contact with VAL2603 (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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2556F CYS* 3.6 28.7 - - + +
2560F LEU* 3.7 29.1 - - + +
2561F PRO* 4.3 9.6 - - + -
2599F ALA 4.1 10.8 - - - +
2600F GLN* 3.2 15.8 + - - +
2602F ASP* 1.3 76.7 - - + +
2604F ILE* 1.3 63.7 + - - +
2606F GLU* 3.3 7.9 + - + +
2607F CYS* 3.2 18.4 + - - +
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Residues in contact with ILE2604 (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* 5.0 13.5 - - - +
2555F LEU* 6.1 3.1 - - + -
2556F CYS* 4.9 4.3 - - + -
2560F LEU* 3.7 24.9 - - + -
2587F VAL* 3.8 17.0 - - + +
2590F LEU* 4.1 30.5 - - + +
2591F SER* 3.7 27.6 - - - -
2596F LEU* 5.4 5.8 - - + -
2600F GLN* 3.6 15.0 - - + +
2601F ARG* 3.3 11.6 + - - +
2603F VAL* 1.3 77.5 - - - +
2605F GLU* 1.3 61.6 + - - +
2607F CYS* 3.2 13.0 + - - +
2608F LEU* 3.5 15.0 + - + +
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Residues in contact with GLU2605 (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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2591F SER* 5.6 2.6 - - - -
2601F ARG 3.1 16.1 + - - +
2602F ASP* 3.8 7.6 - - - +
2603F VAL 3.3 0.2 - - - -
2604F ILE* 1.3 76.9 - - - +
2606F GLU* 1.3 61.4 + - - +
2608F LEU* 3.6 8.8 + - - +
2609F MET* 3.1 23.4 + - - +
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Residues in contact with GLU2606 (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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2564F THR* 4.0 9.5 - - + +
2602F ASP 2.8 17.9 + - - +
2603F VAL* 3.6 10.1 - - + +
2604F ILE 3.2 0.4 - - - -
2605F GLU* 1.3 74.5 - - - +
2607F CYS* 1.3 59.8 + - - +
2609F MET* 3.8 6.3 - - - +
2610F ALA* 3.0 30.8 + - - +
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Residues in contact with CYS2607 (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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2560F LEU* 3.7 36.6 - - + +
2563F ILE* 4.4 13.9 - - - -
2564F THR* 4.5 9.2 - - - +
2584F LEU* 6.5 0.2 - - - -
2587F VAL* 5.3 7.6 - - + -
2603F VAL 3.2 9.0 + - - +
2604F ILE* 3.5 10.5 - - + +
2605F GLU 3.2 0.4 - - - -
2606F GLU* 1.3 75.0 - - - +
2608F LEU* 1.3 71.2 + - + +
2610F ALA 3.4 1.0 + - - -
2611F LEU* 3.1 46.0 + - - +
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Residues in contact with LEU2608 (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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2584F LEU* 3.9 27.8 - - + +
2587F VAL* 3.8 28.0 - - + +
2588F TYR* 4.4 34.5 - - + +
2591F SER* 5.2 6.3 - - - -
2604F ILE 3.5 12.3 + - - +
2605F GLU* 3.6 8.0 + - - +
2606F GLU 3.4 0.2 - - - -
2607F CYS* 1.3 80.6 - - + +
2609F MET* 1.3 63.0 + - - +
2611F LEU* 3.6 11.2 + - + +
2612F CYS* 3.7 10.7 + - - +
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Residues in contact with MET2609 (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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2605F GLU 3.1 18.6 + - - +
2606F GLU* 3.8 7.6 - - - +
2607F CYS 3.2 0.2 - - - -
2608F LEU* 1.3 75.8 - - - +
2610F ALA* 1.3 63.2 + - - +
2612F CYS* 3.4 36.5 + - - +
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Residues in contact with ALA2610 (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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2564F THR* 3.7 29.4 - - + +
2567F ALA* 4.3 18.8 - - + +
2606F GLU 3.0 18.5 + - - +
2607F CYS 4.1 2.0 - - - +
2609F MET* 1.3 77.9 - - - +
2611F LEU* 1.3 61.3 + - + +
2612F CYS* 3.2 4.7 + - - -
2613F ARG* 4.1 9.7 + - - +
2614F TYR* 4.9 3.3 - - - -
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Residues in contact with LEU2611 (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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2563F ILE* 4.4 24.2 - - + +
2564F THR 5.3 0.2 - - - +
2567F ALA* 5.7 4.5 - - + -
2570F PHE* 4.0 33.9 - - + -
2584F LEU* 4.6 24.2 - - + +
2607F CYS* 3.1 40.2 + - - +
2608F LEU* 3.6 9.6 + - + +
2609F MET 3.2 0.6 - - - -
2610F ALA* 1.3 80.8 - - + +
2612F CYS* 1.3 57.6 + - - +
2613F ARG 3.4 3.1 - - - +
2615F ILE* 3.2 39.7 - - + +
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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