Contacts of the helix formed by residues 21 - 30 (chain J) in PDB entry 3Q2K
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 ILE 21 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20J ARG* 1.3 74.4 - - - +
22J SER* 1.3 68.0 + - - +
23J LYS 3.3 0.4 - - - -
24J ASN* 2.9 40.0 + - + +
25J HIS* 3.3 10.1 + - + +
79J ALA* 3.9 19.1 - - + +
102J GLU* 4.5 1.3 - - + -
301J HIS* 4.1 18.8 - - + +
500J NAI 3.0 83.5 + - + +
550J HP7 5.2 4.9 - - - +
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Residues in contact with SER 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J LEU* 3.9 18.2 - - - -
17J GLY 3.5 10.5 - - - -
18J CYS* 3.0 32.6 + - - +
19J GLY 2.4 28.1 + - - +
21J ILE* 1.3 81.3 - - - +
23J LYS* 1.3 63.2 + - - +
25J HIS* 2.6 28.0 + - - +
26J ILE* 2.9 19.2 + - - +
79J ALA* 4.9 0.7 - - - -
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Residues in contact with LYS 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J CYS* 4.7 5.7 + - - -
19J GLY 3.6 18.4 + - - +
20J ARG* 3.4 20.9 - - - +
22J SER* 1.3 85.8 + - - +
24J ASN* 1.3 64.1 + - - +
26J ILE* 3.9 13.8 - - + +
27J GLY* 3.0 21.7 + - - -
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Residues in contact with ASN 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J ARG 5.6 0.6 + - - -
21J ILE* 2.9 35.6 + - + +
23J LYS* 1.3 80.5 - - - +
25J HIS* 1.3 62.5 + - - +
27J GLY* 4.0 0.8 - - - -
28J ALA* 3.2 22.5 + - - +
298J GLY 3.4 19.4 + - - +
299J PHE* 3.8 35.1 - - - -
301J HIS* 3.7 27.3 + - + +
302J PRO* 5.3 1.6 - - - +
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Residues in contact with HIS 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J LEU* 3.6 15.9 - - + -
21J ILE* 3.3 24.6 + - + -
22J SER* 2.6 15.0 + - - +
24J ASN* 1.3 70.8 - - - +
26J ILE* 1.3 65.0 + - - +
28J ALA* 3.0 6.4 + - - +
29J ILE* 3.0 31.4 + - + +
77J VAL* 3.3 20.7 - - + +
79J ALA* 4.6 3.4 - - + -
100J VAL* 5.1 0.2 - - + -
102J GLU* 2.8 37.4 + - - +
129J VAL* 4.2 11.2 - - + -
301J HIS* 3.3 17.7 + + - -
305J TYR* 2.5 35.1 + + - +
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Residues in contact with ILE 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J LEU* 4.5 10.7 - - + +
18J CYS* 5.9 0.2 - - + -
22J SER* 2.9 39.4 + - - +
23J LYS* 3.9 14.4 - - + +
25J HIS* 1.3 71.6 - - - +
27J GLY* 1.3 55.1 + - - +
29J ILE* 3.6 4.9 - - - +
30J ALA* 2.6 43.3 + - + +
38J LEU* 3.8 26.6 - - + +
41J ILE* 6.1 0.7 - - + -
52J ALA* 5.6 10.1 - - + +
55J ALA* 5.3 5.6 - - + +
56J THR* 3.8 24.2 - - + -
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Residues in contact with GLY 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J LYS 3.0 14.3 + - - -
24J ASN* 4.0 1.8 - - - -
26J ILE* 1.3 82.1 - - - +
28J ALA* 1.3 58.4 + - - +
30J ALA* 3.8 6.4 + - - +
31J GLN* 3.1 27.8 + - - +
302J PRO* 5.4 1.6 - - - -
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Residues in contact with ALA 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24J ASN 3.2 16.6 + - - +
25J HIS 3.0 4.4 + - - +
27J GLY* 1.3 72.9 - - - +
29J ILE* 1.3 69.0 - - - +
31J GLN* 3.3 12.8 - - - +
32J HIS* 3.3 17.7 - - - -
301J HIS* 3.8 3.6 - - + -
302J PRO* 3.7 31.6 - - + -
305J TYR* 3.5 30.7 - - + -
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Residues in contact with ILE 29 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J PHE* 3.7 32.8 - - + -
15J LEU* 5.9 2.0 - - + -
25J HIS* 3.0 23.5 + - + +
26J ILE* 3.7 4.5 - - - +
28J ALA* 1.3 72.5 - - - +
30J ALA* 1.3 53.7 - - - +
31J GLN 2.2 21.6 + - - -
32J HIS* 2.7 19.4 + - - +
33J GLY* 3.2 6.6 + - - -
36J ALA* 4.3 9.9 - - + -
37J GLU* 3.9 16.2 - - - +
38J LEU* 3.9 39.9 - - + +
77J VAL* 5.0 3.1 - - + -
305J TYR* 4.0 30.3 - - + +
309J ILE* 6.0 1.1 - - + -
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Residues in contact with ALA 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J ILE* 2.6 33.5 + - + +
27J GLY* 3.9 5.2 - - - +
28J ALA 3.6 0.2 - - - -
29J ILE* 1.3 69.5 - - - +
31J GLN* 1.3 57.2 + - - +
32J HIS 3.8 0.2 - - - -
33J GLY* 4.1 10.7 + - - +
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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