Contacts of the helix formed by residues 2571 - 2587 (chain A) in PDB entry 5NUG
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 THR2571 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2552A VAL* 4.7 4.9 - - - +
2569A VAL* 3.3 16.7 + - + +
2570A PRO* 1.3 80.7 - - - +
2572A LEU* 1.3 66.6 + - - +
2573A ASP* 4.0 4.5 + - - +
2574A THR* 2.1 53.7 + - - +
2575A VAL* 3.4 7.3 + - - +
2743A SER* 6.0 1.8 - - - -
2746A GLN* 4.5 8.7 - - - +
2747A ILE* 3.2 39.9 - - + -
4804A ADP 3.2 13.0 + - - +
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Residues in contact with LEU2572 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2536A ASP* 4.6 18.2 - - + +
2548A TRP* 3.5 26.9 - - + -
2549A GLN* 2.5 57.9 - - + +
2552A VAL* 5.1 3.7 - - - +
2571A THR* 1.3 73.3 - - - +
2573A ASP* 1.3 65.6 + - - +
2575A VAL* 3.4 20.5 - - - +
2576A ARG* 3.5 30.5 + - - +
2746A GLN* 4.8 7.2 - - - +
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Residues in contact with ASP2573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2508A LEU* 5.0 10.7 - - - +
2571A THR* 3.1 6.3 + - - +
2572A LEU* 1.3 83.8 - - - +
2574A THR* 1.3 64.4 + - - +
2576A ARG* 2.4 47.0 + - - +
2577A HIS* 2.9 40.6 + - + -
2739A PRO* 4.2 19.9 - - - +
2743A SER* 4.4 9.4 + - - -
4804A ADP 5.5 3.4 - - - +
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Residues in contact with THR2574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2568A VAL* 4.6 18.3 - - + +
2569A VAL 3.8 4.4 + - - +
2570A PRO* 5.1 2.9 - - + -
2571A THR* 2.1 49.7 + - - +
2573A ASP* 1.3 72.8 - - - +
2575A VAL* 1.3 56.0 + - + +
2577A HIS* 3.2 3.1 + - - +
2578A GLU* 2.7 59.1 + - + +
2604A THR* 4.4 15.7 - - + +
2607A SER* 4.7 2.9 - - - +
4804A ADP 3.2 15.1 + - - +
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Residues in contact with VAL2575 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2548A TRP* 3.5 42.2 - - + +
2551A LYS* 4.6 12.1 - - + +
2552A VAL* 3.7 30.3 - - + -
2570A PRO* 5.3 2.7 - - + -
2571A THR 3.4 7.4 + - - +
2572A LEU* 3.4 18.8 - - - +
2574A THR* 1.3 81.9 - - + +
2576A ARG* 1.3 60.2 + - - +
2578A GLU* 4.0 18.2 - - - +
2579A ALA* 3.3 26.0 + - - +
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Residues in contact with ARG2576 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2496A TYR* 4.3 5.5 + - - -
2500A TRP* 4.0 25.6 - - + -
2508A LEU* 4.3 18.2 - - - +
2511A ARG* 3.7 19.4 - - - +
2535A ILE* 3.6 33.6 + - - +
2536A ASP* 4.4 8.6 + - - -
2548A TRP* 3.3 37.0 - - + +
2572A LEU* 3.5 35.8 + - - +
2573A ASP* 2.4 39.3 + - - +
2575A VAL* 1.3 81.9 - - - +
2577A HIS* 1.3 66.1 + - - +
2579A ALA* 4.2 2.3 - - - +
2580A LEU* 3.6 16.8 + - - +
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Residues in contact with HIS2577 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2500A TRP* 4.3 15.7 - + - -
2508A LEU* 6.3 1.6 - - + -
2511A ARG* 3.8 17.8 + - - -
2573A ASP* 2.9 36.3 + - + -
2574A THR* 3.2 3.6 + - - +
2576A ARG* 1.3 86.9 - - + +
2578A GLU* 1.3 61.2 + - - +
2580A LEU* 3.2 9.7 + - + +
2581A LEU* 2.9 35.0 + - + +
2593A LEU* 6.3 0.2 - - + -
2604A THR* 3.8 18.6 + - + +
2734A VAL* 5.0 13.0 - - + -
2735A TYR 3.4 22.9 + - - -
2736A VAL* 3.9 23.6 - - + +
2737A ASP 5.9 0.2 - - - -
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Residues in contact with GLU2578 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2574A THR* 2.7 34.3 + - - +
2575A VAL* 4.1 13.1 - - - +
2577A HIS* 1.3 77.3 - - - +
2579A ALA* 1.3 57.6 + - - +
2581A LEU* 3.2 4.2 + - - +
2582A TYR* 2.9 27.2 + - + +
2604A THR* 4.0 11.2 - - + +
2607A SER* 2.7 35.7 + - - +
2608A ALA* 3.5 28.1 - - - +
2611A ALA* 6.0 1.4 - - - +
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Residues in contact with ALA2579 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2496A TYR* 4.9 3.1 - - - +
2538A GLU* 5.3 0.9 - - - +
2548A TRP* 3.6 23.3 - - + -
2575A VAL 3.3 17.6 + - - +
2576A ARG 4.2 2.2 - - - +
2578A GLU* 1.3 78.7 - - - +
2580A LEU* 1.3 52.9 + - - +
2582A TYR* 3.2 10.0 + - - +
2583A THR* 2.7 38.0 + - - +
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Residues in contact with LEU2580 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2461A MET* 3.7 18.2 - - + -
2496A TYR* 3.6 15.4 + - + +
2500A TRP* 3.5 63.5 - - + +
2576A ARG 3.6 8.0 + - - +
2577A HIS* 3.2 13.2 + - + +
2579A ALA* 1.3 77.5 - - - +
2581A LEU* 1.3 55.3 + - + +
2583A THR* 3.2 9.6 + - - +
2584A TRP* 2.2 61.5 + - + +
2734A VAL* 4.0 22.9 - - + -
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Residues in contact with LEU2581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2577A HIS* 2.9 14.8 + - + +
2578A GLU 3.5 7.0 - - - +
2580A LEU* 1.3 78.0 - - - +
2582A TYR* 1.3 56.3 + - - +
2584A TRP* 3.2 8.8 + - + +
2585A LEU* 2.9 37.5 + - + +
2591A LEU* 3.7 26.9 - - + -
2593A LEU* 3.5 34.1 - - + -
2604A THR* 3.9 20.9 - - + -
2605A LEU* 3.7 31.0 - - + -
2608A ALA* 3.5 11.7 - - + -
2734A VAL* 4.2 12.6 - - + -
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Residues in contact with TYR2582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2464A GLN* 5.6 5.4 - - - -
2578A GLU* 2.9 12.6 + - + +
2579A ALA* 3.2 13.0 + - - +
2581A LEU* 1.3 75.1 - - - +
2583A THR* 1.3 68.6 + - - +
2585A LEU* 3.2 6.7 + - - +
2586A ALA* 3.1 27.8 + - + +
2608A ALA* 3.7 24.1 - - + +
2611A ALA* 3.5 30.4 + - + -
2612A LEU* 3.7 29.6 - - + +
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Residues in contact with THR2583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2461A MET* 4.4 19.5 - - + -
2464A GLN* 3.2 54.5 - - + +
2493A TYR* 4.1 13.6 + - - +
2496A TYR* 6.2 0.2 - - - -
2579A ALA* 2.7 22.8 + - - +
2580A LEU* 3.2 12.4 + - + +
2582A TYR* 1.3 84.0 - - - +
2584A TRP* 1.3 63.1 + - + +
2585A LEU 3.4 0.2 + - - -
2586A ALA* 3.5 3.6 + - - +
2587A GLU* 3.4 9.3 - - - +
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Residues in contact with TRP2584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2456A GLY 4.6 0.7 - - - -
2457A SER* 2.4 44.2 - - - -
2460A SER* 3.7 14.6 - - - -
2461A MET* 3.0 36.5 - - + +
2501A SER* 5.5 1.6 - - - -
2580A LEU* 2.2 56.4 + - + +
2581A LEU* 3.5 11.0 - - + +
2583A THR* 1.3 80.9 - - + +
2585A LEU* 1.3 64.2 + - - +
2586A ALA 3.6 0.2 + - - -
2587A GLU* 3.6 10.2 + - - +
2589A LYS* 3.6 30.3 + - + +
2590A PRO 4.3 8.5 - - - +
2591A LEU* 4.0 19.5 - - + -
2732A PRO* 2.2 41.7 - - + -
2734A VAL* 5.3 6.8 - - + +
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Residues in contact with LEU2585 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2581A LEU* 2.9 25.9 + - + +
2582A TYR* 3.2 2.6 + - - +
2584A TRP* 1.3 72.5 - - - +
2586A ALA* 1.3 56.7 + - - +
2587A GLU 3.1 2.0 - - - -
2588A HIS* 2.5 30.4 + - - +
2589A LYS 4.6 3.4 - - - +
2591A LEU* 3.8 22.2 - - + -
2605A LEU* 4.7 16.2 - - + -
2608A ALA* 4.8 2.2 - - + -
2609A LEU* 4.8 22.0 - - + +
2612A LEU* 3.3 29.6 - - + -
2615A MET* 3.6 14.3 - - + +
2660A VAL* 5.2 3.1 - - + -
2707A GLN* 3.5 23.3 - - - +
2709A VAL* 3.9 14.6 - - + -
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Residues in contact with ALA2586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2464A GLN* 2.7 33.7 - - - +
2467A ARG* 2.8 26.2 + - - +
2582A TYR* 3.1 20.6 + - + +
2583A THR 3.6 5.2 - - - +
2584A TRP 3.4 0.2 - - - -
2585A LEU* 1.3 76.1 - - - +
2587A GLU* 1.3 52.3 + - - +
2588A HIS* 3.3 16.6 + - - -
2612A LEU* 4.6 10.9 - - + +
2615A MET* 5.1 1.3 - - - -
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Residues in contact with GLU2587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2387A LEU* 5.8 0.7 - - + +
2460A SER* 2.8 55.0 - - - +
2463A HIS* 3.4 17.8 - - + +
2464A GLN* 3.8 12.5 - - + +
2467A ARG* 3.9 22.4 - - - +
2583A THR* 3.4 16.3 - - - +
2584A TRP* 3.6 7.6 + - - +
2585A LEU 3.1 1.2 - - - -
2586A ALA* 1.3 75.0 - - - +
2588A HIS* 1.3 71.2 - - - +
2589A LYS* 3.1 12.9 + - + +
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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
------------------------------------------------------------
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