Contacts of the helix formed by residues 21 - 30 (chain B) in PDB entry 1RRM
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 ALA 21 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A ALA* 6.0 0.4 - - + -
13B TRP* 3.6 47.6 - - + +
17B GLY 4.4 0.6 + - - -
18B ALA 3.0 13.3 + - - +
19B VAL 3.0 1.2 - - - -
20B GLY* 1.3 79.2 - - - +
22B LEU* 1.3 63.0 + - - +
23B THR 3.5 0.9 - - - -
24B ASP* 3.4 10.2 + - + +
25B GLU* 3.1 22.9 + - - +
28B ARG* 4.9 0.6 + - - +
176B PHE* 3.8 2.0 - - + -
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL 3.0 16.5 + - - +
21B ALA* 1.3 78.4 - - - +
23B THR* 1.3 70.1 + - + +
25B GLU* 3.1 3.1 + - - +
26B VAL* 3.0 40.5 + - + +
51B VAL* 4.6 7.4 - - + -
55B MSE 4.1 30.7 - - + -
60B LEU* 5.1 0.2 - - + -
93B ILE* 4.4 13.2 - - + -
136B LEU* 4.2 12.1 - - + -
138B ILE* 3.5 32.1 - - + -
176B PHE* 3.6 31.8 - - + -
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Residues in contact with THR 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL 4.7 0.4 + - - -
20B GLY 4.3 8.9 + - - +
22B LEU* 1.3 83.0 - - + +
24B ASP* 1.3 73.6 + - - +
26B VAL* 3.5 2.1 + - - +
27B LYS* 3.1 31.2 + - - +
54B LYS* 3.6 39.5 - - + +
55B MSE 4.0 3.4 - - - +
58B ALA* 3.7 18.5 - - + +
60B LEU* 3.7 20.9 - - + +
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Residues in contact with ASP 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLY 4.8 5.9 - - - +
21B ALA* 3.4 10.2 + - + +
22B LEU 3.2 0.4 - - - -
23B THR* 1.3 85.3 + - - +
25B GLU* 1.3 61.3 + - - +
27B LYS* 3.5 11.9 + - - +
28B ARG* 3.0 55.4 + - - +
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Residues in contact with GLU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ARG* 4.8 2.8 - - - -
11B THR* 4.1 11.8 - - - +
13B TRP* 2.9 30.9 + - - +
21B ALA 3.1 17.6 + - - +
22B LEU 3.1 7.9 + - - +
24B ASP* 1.3 74.2 - - - +
26B VAL* 1.3 66.2 + - - +
28B ARG* 2.8 33.1 + - - +
29B ARG* 3.2 62.0 + - - +
136B LEU* 5.0 3.1 - - + -
174B VAL* 4.3 3.8 - - + +
176B PHE* 4.0 19.1 - - + -
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Residues in contact with VAL 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 3.0 32.7 + - + +
23B THR 3.7 4.9 - - - +
25B GLU* 1.3 77.0 - - - +
27B LYS* 1.3 62.0 + - - +
29B ARG* 3.1 4.0 + - - +
30B GLY 3.0 18.2 + - - -
31B TYR* 3.5 30.4 + - + +
60B LEU* 4.1 19.7 - - + -
91B TYR* 3.4 35.2 - - + +
136B LEU* 3.7 22.2 - - + -
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B THR* 3.1 23.7 + - - +
24B ASP* 3.8 11.2 - - - +
26B VAL* 1.3 77.8 - - - +
28B ARG* 1.3 63.2 + - + +
30B GLY* 3.2 13.9 + - - +
31B TYR 5.9 0.7 - - - -
58B ALA* 3.1 42.4 + - - -
60B LEU* 4.0 17.1 - - + +
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Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ARG* 5.7 4.4 - - - +
129A ASN 4.5 11.8 - - - +
169A HIS* 5.1 15.2 + - + +
13B TRP* 4.8 7.9 - - - -
21B ALA* 4.9 0.6 + - - +
24B ASP* 3.0 43.6 + - - +
25B GLU* 2.8 47.9 + - - +
26B VAL 3.3 0.4 - - - -
27B LYS* 1.3 77.2 - - + +
29B ARG* 1.3 61.1 + - + +
30B GLY 3.4 0.2 - - - -
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Residues in contact with ARG 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B GLU* 5.3 6.3 + - - -
11B THR* 3.6 17.2 + - - -
25B GLU* 3.2 40.2 + - - +
26B VAL 3.1 4.0 + - - +
28B ARG* 1.3 80.7 - - + +
30B GLY* 1.3 63.3 + - - +
31B TYR* 3.3 50.6 + - + +
136B LEU* 5.0 3.1 - - - -
173B GLN* 4.4 15.4 + - - +
174B VAL* 3.2 34.1 - - - +
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Residues in contact with GLY 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B VAL 3.0 4.2 + - - -
27B LYS* 3.2 13.1 + - - -
28B ARG 3.4 0.4 - - - -
29B ARG* 1.3 78.3 - - - +
31B TYR* 1.3 66.2 + - - +
32B GLN* 3.3 17.1 + - - +
90B ASP* 4.5 0.7 - - - +
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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