Contacts of the helix formed by residues 2597 - 2611 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2549D LEU* 5.7 1.8 - - - +
2552D ASN* 4.1 5.0 + - - -
2553D ARG* 6.0 2.3 - - - +
2596D LEU* 1.3 75.8 - - - +
2598D LYS* 1.3 59.0 + - - +
2599D ALA* 3.5 19.7 - - + +
2600D GLN* 3.1 20.7 + - + +
2601D ARG* 2.8 34.7 + - - +
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Residues in contact with LYS2598 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2596D LEU 3.7 2.6 + - - -
2597D THR* 1.3 74.8 - - - +
2599D ALA* 1.3 62.5 + - - +
2601D ARG* 3.4 18.9 + - - +
2602D ASP* 3.8 5.4 + - - +
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Residues in contact with ALA2599 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2597D THR* 3.2 12.3 - - + +
2598D LYS* 1.3 79.7 - - - +
2600D GLN* 1.3 59.3 + - - +
2601D ARG 3.5 0.5 + - - -
2602D ASP* 3.6 16.6 + - - +
2603D VAL* 4.1 7.8 + - - +
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Residues in contact with GLN2600 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2552D ASN* 5.0 7.6 - - - +
2553D ARG* 5.8 4.7 - - + -
2556D CYS* 3.9 19.1 - - + +
2596D LEU* 5.6 1.6 - - + -
2597D THR* 3.1 26.6 + - + +
2599D ALA* 1.3 76.5 - - - +
2601D ARG* 1.3 64.2 + - - +
2602D ASP 3.3 0.2 - - - -
2603D VAL* 3.2 21.8 + - - +
2604D ILE* 3.4 16.5 + - + +
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Residues in contact with ARG2601 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2591D SER* 6.0 0.3 - - - -
2596D LEU* 5.6 5.8 - - + -
2597D THR 2.8 15.2 + - - +
2598D LYS* 3.5 12.8 - - - +
2599D ALA 3.2 0.6 - - - -
2600D GLN* 1.3 78.7 - - - +
2602D ASP* 1.3 61.3 + - - +
2604D ILE* 3.3 12.7 + - - +
2605D GLU* 3.1 20.8 + - - +
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Residues in contact with ASP2602 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2598D LYS 3.8 5.1 + - - +
2599D ALA* 3.6 11.3 + - - +
2600D GLN 3.3 0.6 - - - -
2601D ARG* 1.3 75.6 - - - +
2603D VAL* 1.3 60.1 + - + +
2605D GLU* 3.4 7.8 + - - +
2606D GLU* 2.8 29.3 + - - +
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Residues in contact with VAL2603 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2556D CYS* 3.6 28.5 - - + +
2560D LEU* 3.7 28.8 - - + +
2561D PRO* 4.3 9.6 - - + -
2599D ALA 4.1 11.2 - - - +
2600D GLN* 3.2 15.6 + - - +
2602D ASP* 1.3 76.0 - - + +
2604D ILE* 1.3 64.7 + - - +
2606D GLU* 3.3 8.7 + - + +
2607D CYS* 3.2 17.8 + - - +
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Residues in contact with ILE2604 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2552D ASN* 5.0 14.4 - - - +
2555D LEU* 6.1 2.9 - - + -
2556D CYS* 4.9 4.5 - - + -
2560D LEU* 3.7 24.5 - - + -
2587D VAL* 3.8 17.7 - - + +
2590D LEU* 4.1 31.0 - - + +
2591D SER* 3.7 27.8 - - - -
2596D LEU* 5.4 5.2 - - + -
2600D GLN* 3.6 14.8 - - + +
2601D ARG* 3.3 10.7 + - - +
2603D VAL* 1.3 77.9 - - - +
2605D GLU* 1.3 61.2 + - - +
2607D CYS* 3.2 13.3 + - + +
2608D LEU* 3.5 14.4 + - + +
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Residues in contact with GLU2605 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2591D SER* 5.6 2.9 - - - -
2601D ARG 3.1 15.2 + - - +
2602D ASP* 3.8 7.9 - - - +
2603D VAL 3.3 0.2 - - - -
2604D ILE* 1.3 77.3 - - - +
2606D GLU* 1.3 62.4 + - - +
2608D LEU* 3.6 9.0 + - - +
2609D MET* 3.1 23.6 + - - +
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Residues in contact with GLU2606 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2564D THR* 4.0 9.5 - - + +
2602D ASP 2.8 17.9 + - - +
2603D VAL* 3.6 9.2 - - + +
2604D ILE 3.2 0.4 - - - -
2605D GLU* 1.3 74.5 - - - +
2607D CYS* 1.3 60.4 + - - +
2609D MET* 3.8 6.7 - - - +
2610D ALA* 3.0 30.5 + - - +
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Residues in contact with CYS2607 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2560D LEU* 3.7 36.3 - - + +
2563D ILE* 4.4 14.8 - - - -
2564D THR* 4.5 9.4 - - - +
2584D LEU* 6.5 0.4 - - - -
2587D VAL* 5.3 7.4 - - + -
2603D VAL 3.2 9.9 + - - +
2604D ILE* 3.5 9.9 - - + +
2605D GLU 3.2 0.8 - - - -
2606D GLU* 1.3 74.5 - - - +
2608D LEU* 1.3 70.9 + - + +
2610D ALA* 3.4 0.7 + - - -
2611D LEU* 3.1 44.7 + - - +
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Residues in contact with LEU2608 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2584D LEU* 3.9 27.6 - - + +
2587D VAL* 3.8 27.6 - - + +
2588D TYR* 4.4 33.9 - - + +
2591D SER* 5.2 6.5 - - - -
2604D ILE* 3.5 12.4 + - + +
2605D GLU* 4.1 9.0 - - - +
2606D GLU 3.4 0.2 - - - -
2607D CYS* 1.3 80.3 - - + +
2609D MET* 1.3 61.9 + - - +
2611D LEU* 3.6 10.9 + - + +
2612D CYS* 3.7 10.7 + - - +
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Residues in contact with MET2609 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2605D GLU 3.1 18.8 + - - +
2606D GLU* 3.8 7.9 - - - +
2607D CYS 3.2 0.4 - - - -
2608D LEU* 1.3 75.3 - - - +
2610D ALA* 1.3 65.7 + - - +
2612D CYS* 3.4 35.8 + - - +
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Residues in contact with ALA2610 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2564D THR* 3.7 29.2 - - + +
2567D ALA* 4.3 19.3 - - + +
2606D GLU 3.0 18.8 + - - +
2607D CYS 4.1 2.0 - - - +
2609D MET* 1.3 78.2 - - - +
2611D LEU* 1.3 61.8 + - + +
2612D CYS* 3.2 4.1 + - - -
2613D ARG* 4.1 9.4 + - - +
2614D TYR* 4.9 3.6 - - - -
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Residues in contact with LEU2611 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2563D ILE* 4.4 24.9 - - + +
2564D THR 5.3 0.2 - - - +
2567D ALA* 5.7 4.3 - - + -
2570D PHE* 4.0 35.4 - - + -
2584D LEU* 4.6 23.4 - - + +
2607D CYS* 3.1 39.2 + - - +
2608D LEU* 3.9 10.1 - - - +
2609D MET 3.2 0.8 - - - -
2610D ALA* 1.3 81.5 - - + +
2612D CYS* 1.3 57.6 + - - +
2613D ARG 3.4 3.8 - - - +
2615D ILE* 3.2 40.0 - - + +
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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