Contacts of the helix formed by residues 19 - 30 (chain A) in PDB entry 1RGD
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 GLY 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLU 4.8 1.0 + - - -
8A ALA* 4.7 4.2 - - - +
9A SER* 5.1 4.0 - - - +
17A THR 3.4 2.6 + - - -
18A CYS* 1.3 70.6 - - - +
20A SER* 1.3 64.6 + - - +
22A LYS* 3.1 31.3 - - - +
23A VAL* 3.1 16.5 + - - +
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Residues in contact with SER 20 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ASP* 4.8 1.4 + - - -
18A CYS* 3.2 22.3 - - - +
19A GLY* 1.3 71.0 - - - +
21A CYS* 1.3 53.8 + - - -
22A LYS 2.8 4.2 + - - -
23A VAL* 3.0 6.3 + - - +
24A PHE* 2.8 38.8 + - - +
57A ARG* 4.1 6.9 + - - -
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Residues in contact with CYS 21 (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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1A CYS* 4.1 4.0 - - - -
17A THR* 3.4 16.6 - - - +
18A CYS* 2.9 11.0 + - - +
20A SER* 1.3 74.2 + - - +
22A LYS* 1.3 54.9 + - - +
24A PHE* 3.3 19.5 - - + +
25A PHE* 3.0 26.3 + - - +
57A ARG* 3.1 29.8 - - - -
61A CYS* 3.7 18.7 - - - -
66A MET* 4.6 0.6 - - - +
72A ZN 2.6 36.6 - - - -
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Residues in contact with LYS 22 (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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9A SER* 2.9 18.1 + - - -
10A GLY 2.8 28.0 + - - -
11A CYS* 3.2 20.3 - - + +
13A TYR* 3.2 53.6 - - + +
15A VAL 4.6 7.9 - - - +
17A THR* 4.0 11.0 - - - +
18A CYS 3.9 6.1 - - - +
19A GLY* 3.1 22.6 - - - +
20A SER 2.8 0.8 + - - -
21A CYS* 1.3 74.2 - - - +
23A VAL* 1.3 58.9 + - + +
24A PHE 3.1 0.7 - - - -
25A PHE* 3.0 5.2 + - - +
26A LYS 2.8 29.5 + - - -
66A MET* 4.0 10.8 - - + -
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Residues in contact with VAL 23 (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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13A TYR* 4.0 11.7 - - - +
19A GLY* 3.2 17.9 - - - +
20A SER* 3.0 6.7 + - - +
22A LYS* 1.3 80.1 - - + +
24A PHE* 1.3 52.9 - - - +
26A LYS* 3.1 28.2 + - - +
27A ARG* 2.9 59.3 + - - +
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Residues in contact with PHE 24 (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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20A SER* 2.8 18.7 + - - +
21A CYS* 3.3 23.3 - - - +
23A VAL* 1.3 71.5 - - - +
25A PHE* 1.3 71.9 + - - +
27A ARG* 3.0 7.8 + - - +
28A ALA* 2.8 20.6 + - - +
35A TYR* 3.2 40.2 + + - -
51A LYS* 5.9 0.9 - - + -
54A PRO* 4.3 2.9 - - + -
57A ARG* 3.7 33.7 - - + -
58A TYR* 3.6 36.3 - + + -
61A CYS* 4.7 1.6 - - - -
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Residues in contact with PHE 25 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A CYS 3.0 11.4 + - - +
22A LYS 3.1 10.1 - - - +
24A PHE* 1.3 83.0 - + - +
26A LYS* 1.3 55.9 + - - +
28A ALA* 2.8 2.6 - - - +
29A VAL* 2.6 58.5 + - + +
58A TYR* 3.2 49.8 - + + -
61A CYS* 4.5 7.9 - - + -
62A LEU* 3.7 16.8 - - + -
66A MET* 3.4 30.5 - - + -
67A ASN* 3.2 17.7 - - - -
68A LEU* 3.1 39.5 - - + -
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A TYR* 3.4 25.6 - - + +
22A LYS 2.8 13.2 + - - +
23A VAL* 3.1 45.4 + - - +
25A PHE* 1.3 76.4 - - - +
27A ARG* 1.3 84.8 + - - +
29A VAL* 3.2 2.1 + - - +
30A GLU* 2.9 62.5 + - - +
68A LEU* 3.4 31.2 - - + -
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Residues in contact with ARG 27 (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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23A VAL* 2.9 41.4 + - - +
24A PHE* 3.9 4.5 - - - +
26A LYS* 1.3 87.1 - - - +
28A ALA* 1.3 54.1 + - - +
30A GLU* 3.3 13.7 - - - +
31A GLY* 2.9 29.1 + - - -
32A GLN* 3.8 2.3 + - - +
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Residues in contact with ALA 28 (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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24A PHE 2.8 15.5 + - - +
25A PHE* 2.8 15.7 - - - +
27A ARG* 1.3 65.9 - - - +
29A VAL* 1.3 62.4 + - - +
30A GLU 3.1 0.4 - - - -
31A GLY 2.9 15.2 + - - -
32A GLN* 2.9 32.0 - - - +
33A HIS* 3.1 2.7 + - - -
35A TYR* 3.1 36.1 - - + +
58A TYR* 3.8 9.6 - - + -
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Residues in contact with VAL 29 (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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25A PHE* 2.6 68.5 + - + +
26A LYS* 3.3 6.1 - - - +
28A ALA* 1.3 71.2 - - - +
30A GLU* 1.3 61.6 - - - +
33A HIS* 3.6 27.8 - - + +
58A TYR* 3.9 7.4 - - - +
67A ASN* 5.4 1.8 - - - +
68A LEU* 4.0 20.2 - - + -
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Residues in contact with GLU 30 (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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26A LYS* 2.9 52.4 + - - +
27A ARG* 3.3 20.2 - - - +
29A VAL* 1.3 79.9 - - - +
31A GLY* 1.3 59.3 + - - +
33A HIS* 5.2 0.4 - - - -
68A LEU* 4.4 7.8 - - - +
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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