Contacts of the helix formed by residues 14 - 25 (chain A) in PDB entry 1RLI
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 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A SER* 3.2 11.9 + - - -
13A GLY* 1.3 81.0 - - - +
15A ASN* 1.3 67.3 + - - -
16A THR 3.3 2.7 - - - -
17A ASP* 3.1 11.1 + - - -
18A VAL* 2.9 23.3 + - - +
158A PRO* 5.5 11.0 - - - -
159A GLY 5.7 1.3 - - - -
606A PT 4.5 0.2 - - - -
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Residues in contact with ASN 15 (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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14A GLY* 1.3 71.2 - - - -
16A THR* 1.3 62.5 + - - +
18A VAL* 3.3 3.3 + - - +
19A LEU* 3.2 23.2 + - - +
120A VAL* 3.8 17.0 - - + +
155A GLY* 3.7 23.0 + - - -
156A ASN 4.5 1.0 - - - -
157A ARG 3.0 26.2 + - - +
158A PRO* 4.2 2.5 - - - +
159A GLY 3.1 23.6 + - - +
161A ILE* 3.1 37.9 + - + +
606A PT 3.7 11.1 - - - -
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Residues in contact with THR 16 (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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7A ASN* 4.6 8.3 - - - +
14A GLY 3.3 0.6 - - - -
15A ASN* 1.3 78.3 - - - +
17A ASP* 1.3 60.1 + - - +
19A LEU* 3.4 2.3 + - - +
20A ALA* 3.0 27.6 + - - +
75A ALA* 3.9 16.2 - - + +
76A THR* 3.7 30.7 + - - +
77A PRO* 3.4 23.6 - - + +
118A ILE* 4.5 6.7 - - + +
120A VAL* 3.6 17.3 - - + +
606A PT 3.3 16.4 - - - -
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Residues in contact with ASP 17 (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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7A ASN* 2.6 38.7 + - - +
10A THR 3.3 16.8 - - - +
11A ARG* 5.1 0.4 - - - -
12A SER* 3.4 3.3 + - - -
13A GLY* 3.1 28.2 + - - +
14A GLY* 3.1 16.6 + - - +
16A THR* 1.3 77.2 - - - +
18A VAL* 1.3 66.1 + - - +
20A ALA* 3.4 3.3 + - - +
21A GLU* 2.9 25.8 + - - +
33A TYR* 3.8 14.2 + - - +
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLY* 4.2 11.4 - - - +
14A GLY 2.9 21.8 + - - +
15A ASN* 3.7 7.4 - - - +
16A THR 3.3 0.4 - - - -
17A ASP* 1.3 77.4 - - - +
19A LEU* 1.3 63.3 + - - +
21A GLU* 3.3 5.9 + - - +
22A LYS* 3.1 35.5 + - + +
159A GLY* 6.2 1.6 - - - +
161A ILE* 3.8 21.3 - - + -
162A LEU* 4.2 25.8 - - + -
168A LEU* 4.7 2.9 - - + -
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Residues in contact with LEU 19 (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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15A ASN 3.2 13.1 + - - +
16A THR 3.8 3.6 - - - +
18A VAL* 1.3 80.3 - - - +
20A ALA* 1.3 63.2 + - - +
22A LYS* 3.3 14.3 + - + +
23A ALA 3.4 7.8 + - - -
118A ILE* 3.8 20.5 - - + +
120A VAL* 3.5 24.9 - - + -
151A VAL* 4.1 16.6 - - + +
153A GLY* 4.1 13.9 - - - +
161A ILE* 4.1 7.9 - - + -
167A ALA* 3.6 30.7 - - + +
168A LEU* 3.9 19.5 - - + +
171A ALA* 3.6 22.0 - - + +
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Residues in contact with ALA 20 (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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5A VAL* 4.2 17.5 - - + -
7A ASN* 5.1 2.0 - - - +
16A THR 3.0 18.3 + - - +
17A ASP* 3.8 6.7 - - - +
18A VAL 3.3 0.2 - - - -
19A LEU* 1.3 76.4 - - - +
21A GLU* 1.3 63.7 + - - +
23A ALA* 3.0 13.7 + - - +
24A VAL* 3.2 18.4 + - - +
31A HIS* 6.3 2.0 - - + -
73A ILE* 5.4 0.6 - - + +
75A ALA* 4.2 18.2 - - + -
118A ILE* 3.5 19.0 - - + +
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Residues in contact with GLU 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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17A ASP 2.9 18.3 + - - +
18A VAL* 3.7 6.3 - - - +
20A ALA* 1.3 77.3 - - - +
22A LYS* 1.3 64.8 + - + +
24A VAL* 3.2 7.4 + - - +
25A GLN* 3.0 45.4 + - + +
31A HIS* 3.2 30.2 + - - -
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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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18A VAL* 3.1 23.1 + - + +
19A LEU* 3.4 13.0 - - + +
20A ALA 3.2 0.2 - - - -
21A GLU* 1.3 77.2 - - + +
23A ALA* 1.3 60.3 + - - +
25A GLN* 4.0 26.4 + - - +
162A LEU* 4.4 18.1 - - - +
168A LEU* 4.2 35.9 - - + +
171A ALA* 4.0 12.1 - - + -
172A SER* 3.7 22.7 + - - +
176A LYS* 4.9 2.8 + - - -
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Residues in contact with ALA 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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19A LEU 3.4 2.7 + - - +
20A ALA 3.0 9.6 + - - +
22A LYS* 1.3 82.6 - - - +
24A VAL* 1.3 58.9 + - - +
25A GLN 3.4 0.6 + - - -
27A PHE* 3.9 8.7 - - - -
73A ILE* 4.6 8.3 - - + -
118A ILE* 3.9 23.1 - - + -
171A ALA 3.1 23.3 + - - +
174A LEU* 4.2 13.9 - - + -
175A LEU* 3.4 19.6 + - + +
176A LYS* 4.7 4.9 + - - -
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Residues in contact with VAL 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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3A ILE* 4.0 15.3 - - + -
5A VAL* 3.8 17.5 - - + -
20A ALA 3.2 14.1 + - - +
21A GLU* 3.8 24.0 - - - +
23A ALA* 1.3 76.7 - - - +
25A GLN* 1.3 67.5 + - - +
26A GLY 3.2 0.3 + - - -
27A PHE* 2.9 25.1 + - + +
28A ASP 3.9 3.6 + - - -
29A ALA* 3.9 12.3 + - + +
31A HIS* 4.0 13.9 - - + +
73A ILE* 3.6 31.2 - - + -
175A LEU* 4.1 0.4 - - + -
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Residues in contact with GLN 25 (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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21A GLU* 3.0 25.8 + - + +
22A LYS* 4.1 28.2 + - - +
23A ALA 3.4 2.2 - - - -
24A VAL* 1.3 77.6 - - - +
26A GLY* 1.3 61.6 + - - +
27A PHE* 3.3 14.9 - - - -
176A LYS* 4.7 8.0 + - - +
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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