Contacts of the helix formed by residues 2597 - 2611 (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 THR2597 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2549B LEU* 5.7 1.6 - - - +
2552B ASN* 4.1 5.4 + - - -
2553B ARG* 6.0 1.9 - - - +
2596B LEU* 1.3 75.7 - - - +
2598B LYS* 1.3 57.4 + - + +
2599B ALA* 3.5 20.2 - - + +
2600B GLN* 3.1 19.9 + - + +
2601B ARG* 2.8 34.9 + - - +
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Residues in contact with LYS2598 (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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2596B LEU 3.7 3.2 + - - -
2597B THR* 1.3 73.8 - - + +
2599B ALA* 1.3 61.1 + - - +
2601B ARG* 3.4 19.6 + - - +
2602B ASP* 3.8 5.7 + - - +
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Residues in contact with ALA2599 (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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2597B THR* 3.2 12.7 - - + +
2598B LYS* 1.3 79.5 - - - +
2600B GLN* 1.3 59.7 + - - +
2601B ARG 3.5 0.3 + - - -
2602B ASP* 3.6 16.0 + - - +
2603B VAL* 4.1 8.4 + - - +
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Residues in contact with GLN2600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2552B ASN* 5.0 7.4 - - - +
2553B ARG* 5.8 4.5 - - - -
2556B CYS* 3.9 19.1 - - + +
2596B LEU* 5.6 1.6 - - + -
2597B THR* 3.1 26.9 + - + +
2599B ALA* 1.3 77.6 - - - +
2601B ARG* 1.3 64.6 + - - +
2602B ASP 3.3 0.2 - - - -
2603B VAL* 3.2 20.9 + - - +
2604B ILE* 3.4 17.2 + - + +
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Residues in contact with ARG2601 (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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2591B SER* 6.0 0.2 - - - -
2596B LEU* 5.6 5.6 - - + -
2597B THR 2.8 15.5 + - - +
2598B LYS* 3.5 13.2 - - - +
2599B ALA 3.2 0.6 - - - -
2600B GLN* 1.3 78.7 - - - +
2602B ASP* 1.3 60.7 + - - +
2604B ILE* 3.3 12.7 + - - +
2605B GLU* 3.1 21.5 + - - +
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Residues in contact with ASP2602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2598B LYS 3.8 4.9 + - - +
2599B ALA* 3.6 11.3 + - - +
2600B GLN 3.3 0.6 - - - -
2601B ARG* 1.3 75.8 - - - +
2603B VAL* 1.3 60.7 + - + +
2605B GLU* 3.7 7.7 - - - +
2606B GLU* 2.8 30.1 + - - +
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Residues in contact with VAL2603 (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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2556B CYS* 3.6 27.8 - - + +
2560B LEU* 3.7 29.1 - - + +
2561B PRO* 4.3 9.2 - - + -
2599B ALA 4.1 11.0 - - - +
2600B GLN* 3.2 15.8 + - - +
2602B ASP* 1.3 76.8 - - + +
2604B ILE* 1.3 63.6 + - - +
2606B GLU* 3.3 7.8 + - + +
2607B CYS* 3.2 17.7 + - - +
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Residues in contact with ILE2604 (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* 5.0 14.1 - - - +
2555B LEU* 6.1 3.1 - - + -
2556B CYS* 4.9 4.0 - - + -
2560B LEU* 3.7 24.7 - - + -
2587B VAL* 3.8 17.9 - - + +
2590B LEU* 4.1 31.0 - - + +
2591B SER* 3.7 27.6 - - - +
2596B LEU* 5.4 4.9 - - + -
2600B GLN* 3.6 14.8 - - + +
2601B ARG* 3.3 11.1 + - - +
2603B VAL* 1.3 77.1 - - - +
2605B GLU* 1.3 60.8 + - - +
2607B CYS* 3.2 12.2 + - + +
2608B LEU* 3.5 14.8 + - + +
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Residues in contact with GLU2605 (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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2591B SER* 5.6 3.3 - - - -
2601B ARG 3.1 15.6 + - - +
2602B ASP* 3.8 8.3 - - - +
2604B ILE* 1.3 76.9 - - - +
2606B GLU* 1.3 61.5 + - - +
2608B LEU* 3.6 8.9 + - - +
2609B MET* 3.1 23.4 + - - +
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Residues in contact with GLU2606 (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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2564B THR* 4.0 9.2 - - + +
2602B ASP 2.8 17.9 + - - +
2603B VAL* 3.6 9.9 - - + +
2604B ILE 3.2 0.2 - - - -
2605B GLU* 1.3 74.3 - - - +
2607B CYS* 1.3 58.8 + - - +
2609B MET* 3.8 6.3 - - - +
2610B ALA* 3.0 30.5 + - - +
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Residues in contact with CYS2607 (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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2560B LEU* 3.7 36.8 - - + +
2563B ILE* 4.4 14.6 - - - -
2564B THR* 4.5 9.6 - - - +
2584B LEU* 6.5 0.4 - - - -
2587B VAL* 5.3 7.4 - - + -
2603B VAL 3.2 9.4 + - - +
2604B ILE* 3.5 9.9 - - + +
2605B GLU 3.2 0.4 - - - -
2606B GLU* 1.3 75.0 - - - +
2608B LEU* 1.3 71.1 + - + +
2610B ALA 3.4 0.9 + - - -
2611B LEU* 3.1 45.5 + - - +
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Residues in contact with LEU2608 (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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2584B LEU* 3.9 27.4 - - + +
2587B VAL* 3.8 27.6 - - + +
2588B TYR* 4.4 34.1 - - + +
2591B SER* 5.2 6.3 - - - -
2604B ILE 3.5 11.5 + - - +
2605B GLU* 3.6 9.4 + - - +
2607B CYS* 1.3 80.4 - - + +
2609B MET* 1.3 61.4 + - - +
2611B LEU* 3.6 10.8 + - - +
2612B CYS* 3.7 10.9 + - - +
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Residues in contact with MET2609 (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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2605B GLU 3.1 18.4 + - - +
2606B GLU* 3.8 7.4 - - - +
2607B CYS 3.2 0.2 - - - -
2608B LEU* 1.3 76.5 - - - +
2610B ALA* 1.3 64.0 + - - +
2612B CYS* 3.4 35.6 + - - +
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Residues in contact with ALA2610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2564B THR* 3.7 29.4 - - + +
2567B ALA* 4.3 19.1 - - + +
2606B GLU 3.0 18.3 + - - +
2607B CYS 3.4 2.0 + - - +
2609B MET* 1.3 76.5 - - - +
2611B LEU* 1.3 60.3 + - + +
2612B CYS* 3.2 5.2 + - - -
2613B ARG* 4.1 9.0 + - - +
2614B TYR* 4.9 3.3 - - - -
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Residues in contact with LEU2611 (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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2563B ILE* 4.4 24.7 - - + +
2567B ALA* 5.7 4.5 - - + -
2570B PHE* 4.0 35.7 - - + -
2584B LEU* 4.6 23.8 - - + +
2607B CYS* 3.1 39.6 + - - +
2608B LEU* 3.9 9.0 - - - +
2609B MET 3.2 0.8 - - - -
2610B ALA* 1.3 82.0 - - + +
2612B CYS* 1.3 56.9 + - - -
2613B ARG 3.4 2.2 - - - +
2615B ILE* 3.2 40.1 - - + +
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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