Contacts of the helix formed by residues 2493 - 2510 (chain A) in PDB entry 5ZCS
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 LEU2493 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2428A ASN* 3.9 36.3 - - + +
2431A LEU* 3.8 39.2 - - + +
2492A ALA* 1.3 83.5 - - + +
2494A ASN* 1.3 59.5 + - - +
2495A LYS 3.3 0.2 - - - -
2496A LYS* 3.9 3.6 - - + +
2497A ALA* 2.9 35.5 + - + +
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Residues in contact with ASN2494 (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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1809A GLN* 4.4 17.8 + - - +
1814A LYS* 5.4 10.1 - - - +
2492A ALA 3.3 6.1 - - - +
2493A LEU* 1.3 80.4 - - - +
2495A LYS* 1.3 60.0 + - - +
2496A LYS 3.6 0.3 + - - -
2497A ALA* 4.7 2.2 - - - +
2498A ILE* 3.3 39.4 + - - +
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Residues in contact with LYS2495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1814A LYS* 4.7 17.3 - - - +
2492A ALA* 3.6 14.2 + - - +
2493A LEU 3.3 0.4 - - - -
2494A ASN* 1.3 79.5 - - - +
2496A LYS* 1.3 61.8 + - - +
2498A ILE* 4.1 2.4 + - - +
2499A GLN* 3.3 45.6 + - - +
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Residues in contact with LYS2496 (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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2362A PHE 4.7 3.0 - - - -
2363A GLU* 3.7 33.4 + - - +
2431A LEU* 3.8 44.4 - - + -
2434A THR* 5.9 2.7 - - - +
2492A ALA 3.6 13.2 + - - +
2493A LEU* 3.5 4.5 + - + +
2494A ASN 3.3 0.2 - - - -
2495A LYS* 1.3 79.4 - - - +
2497A ALA* 1.3 59.8 + - - +
2498A ILE 3.3 0.4 - - - -
2499A GLN* 3.2 14.3 + - + +
2500A ILE* 2.9 49.0 + - + +
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Residues in contact with ALA2497 (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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2422A VAL* 4.7 16.6 - - + +
2423A TYR* 5.1 15.3 - - + +
2431A LEU* 5.3 4.0 - - + +
2493A LEU* 2.9 20.9 + - + +
2494A ASN* 4.7 2.9 - - - +
2495A LYS 3.6 0.2 - - - -
2496A LYS* 1.3 76.9 - - - +
2498A ILE* 1.3 63.0 + - + +
2500A ILE* 3.9 11.0 + - - +
2501A ILE* 3.5 30.1 + - - +
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Residues in contact with ILE2498 (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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1806A HIS* 5.1 14.8 - - + +
1809A GLN* 3.3 29.8 - - + +
1814A LYS* 4.8 13.5 - - - +
2494A ASN* 3.3 32.8 + - - +
2495A LYS 4.5 2.7 - - - +
2496A LYS 3.3 0.4 - - - -
2497A ALA* 1.3 78.8 - - + +
2499A GLN* 1.3 58.8 + - + +
2501A ILE* 3.3 6.8 + - - +
2502A ASN* 2.8 47.0 + - - +
2505A ARG* 4.8 1.9 + - - +
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Residues in contact with GLN2499 (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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2495A LYS* 3.3 45.4 + - - +
2496A LYS* 3.2 17.1 + - + +
2498A ILE* 1.3 76.0 - - + +
2500A ILE* 1.3 61.1 + - - +
2502A ASN* 3.5 14.3 - - - +
2503A ARG* 2.9 28.9 + - - +
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Residues in contact with ILE2500 (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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2362A PHE* 3.6 44.5 - - + -
2418A LEU* 5.4 2.9 - - + -
2422A VAL* 4.8 23.3 - - + -
2430A ARG* 5.9 2.2 - - - +
2431A LEU* 4.2 17.7 - - + -
2496A LYS* 2.9 51.5 + - + +
2497A ALA* 4.0 9.0 - - - +
2499A GLN* 1.3 77.0 - - - +
2501A ILE* 1.3 63.8 + - + +
2503A ARG* 3.2 7.8 + - - +
2504A VAL* 2.9 32.9 + - + +
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Residues in contact with ILE2501 (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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2415A MET* 4.2 23.1 - - + -
2418A LEU* 4.6 16.2 - - + +
2419A GLU* 5.3 8.5 - - + +
2422A VAL* 5.7 6.5 - - + -
2423A TYR* 3.5 34.1 - - + +
2497A ALA 3.5 14.8 + - - +
2498A ILE* 3.3 7.4 + - - +
2500A ILE* 1.3 79.8 - - + +
2502A ASN* 1.3 59.9 + - - +
2504A VAL* 3.7 6.0 - - + +
2505A ARG* 2.9 52.4 + - + +
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Residues in contact with ASN2502 (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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1806A HIS* 5.3 5.7 - - - -
2498A ILE* 2.8 43.7 + - - +
2499A GLN* 3.5 15.4 - - + +
2501A ILE* 1.3 76.2 - - - +
2503A ARG* 1.3 57.5 + - - +
2505A ARG* 2.4 36.5 + - - +
2506A ASP* 2.9 41.3 + - - +
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Residues in contact with ARG2503 (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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2362A PHE* 6.0 5.4 - - + -
2499A GLN 2.9 18.6 + - - +
2500A ILE* 3.6 6.3 - - - +
2502A ASN* 1.3 72.6 - - - +
2504A VAL* 1.3 61.1 + - + +
2506A ASP* 3.4 28.3 + - - +
2507A LYS* 2.9 61.2 + - + +
2511A ARG 4.5 0.2 + - - -
2512A ASP* 3.4 36.0 + - - +
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Residues in contact with VAL2504 (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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2333A ILE* 4.5 21.9 - - + +
2362A PHE* 4.0 24.7 - - + -
2414A VAL 5.8 0.4 - - - +
2415A MET* 4.5 10.3 - - + -
2418A LEU* 3.8 33.4 - - + -
2500A ILE* 2.9 21.0 + - + +
2501A ILE* 3.7 5.8 - - - +
2502A ASN 3.3 0.2 - - - -
2503A ARG* 1.3 76.2 - - + +
2505A ARG* 1.3 57.0 + - - +
2507A LYS* 3.3 6.4 + - - +
2508A LEU* 2.9 44.7 + - + +
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Residues in contact with ARG2505 (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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1806A HIS* 5.4 7.7 + - - -
2415A MET* 4.9 15.7 - - + +
2498A ILE* 4.8 3.4 + - - +
2501A ILE* 2.9 45.8 + - + +
2502A ASN* 2.4 37.6 + - - +
2504A VAL* 1.3 74.9 - - - +
2506A ASP* 1.3 60.7 + - - +
2508A LEU* 3.3 8.2 + - + +
2509A THR* 2.9 36.6 + - + +
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Residues in contact with ASP2506 (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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2502A ASN* 2.9 28.6 + - - +
2503A ARG* 3.4 29.0 + - - +
2504A VAL 3.3 0.2 - - - -
2505A ARG* 1.3 81.3 - - - +
2507A LYS* 1.3 57.9 + - - +
2509A THR* 3.5 8.1 + - - +
2510A GLY* 3.1 19.1 + - - -
2511A ARG* 3.3 31.1 + - - +
2512A ASP* 4.2 0.5 + - - +
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Residues in contact with LYS2507 (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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2332A TYR* 2.5 63.0 + - + +
2333A ILE* 3.7 28.8 - - + +
2503A ARG* 2.9 54.9 + - + +
2504A VAL* 3.9 4.3 - - - +
2506A ASP* 1.3 76.0 - - - +
2508A LEU* 1.3 62.8 + - - +
2509A THR 3.4 0.2 - - - -
2510A GLY* 3.5 8.6 + - - +
2512A ASP* 3.5 17.2 + - + +
2513A PHE* 5.4 3.6 - - - -
2524A GLN* 3.7 15.4 + - - -
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Residues in contact with LEU2508 (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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2333A ILE* 4.0 25.4 - - + -
2404A MET* 6.1 0.2 - - - +
2407A LEU* 4.3 18.8 - - + +
2408A ARG* 4.2 29.8 + - + +
2411A LYS* 6.5 0.7 - - + -
2414A VAL* 4.3 25.4 - - + +
2415A MET* 4.4 11.9 - - + -
2504A VAL* 2.9 37.7 + - + +
2505A ARG* 3.8 7.6 - - + +
2507A LYS* 1.3 79.0 - - - +
2509A THR* 1.3 61.9 + - + +
2510A GLY 3.6 0.2 + - - -
2524A GLN* 4.8 3.7 + - - +
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Residues in contact with THR2509 (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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2408A ARG* 5.5 2.9 + - - -
2505A ARG* 2.9 23.5 + - + +
2506A ASP* 3.3 13.7 + - - -
2508A LEU* 1.3 78.4 - - + +
2510A GLY* 1.3 60.1 + - - +
2511A ARG* 3.4 22.6 + - - +
2518A THR* 4.2 20.9 - - - +
2519A LEU 4.6 5.7 + - - +
2524A GLN* 5.1 2.3 - - - +
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Residues in contact with GLY2510 (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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2506A ASP 3.1 9.2 + - - -
2507A LYS* 3.5 8.9 + - - -
2508A LEU 3.3 3.2 - - - -
2509A THR* 1.3 78.3 - - - +
2511A ARG* 1.3 56.8 + - - +
2512A ASP* 3.2 21.9 + - - +
2513A PHE 4.9 0.2 + - - -
2519A LEU* 4.8 16.1 + - - +
2524A GLN* 4.1 20.1 - - - +
2527A LEU* 4.7 9.2 - - - +
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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
------------------------------------------------------------
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