Contacts of the helix formed by residues 23 - 36 (chain B) in PDB entry 3RLQ
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 GLN 23 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ALA 3.7 1.2 + - - -
22B PHE* 1.3 74.0 - - - +
24B ALA* 1.3 81.4 + - - +
25B GLU* 2.7 55.1 + - - +
26B ILE* 3.1 10.5 + - + +
27B ALA* 3.0 16.5 + - - +
108B GLY 2.7 18.4 + - - +
109B THR* 3.6 23.6 - - - +
110B ILE 4.2 1.1 - - - +
111B ALA* 3.3 22.3 - - - +
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Residues in contact with ALA 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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22B PHE 3.6 3.0 + - - -
23B GLN* 1.3 83.3 - - - +
25B GLU* 1.3 61.2 + - - +
27B ALA* 3.2 7.7 + - - +
28B GLN* 3.0 41.0 + - + +
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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
----------------------------------------------------------
23B GLN* 2.7 33.0 + - - +
24B ALA* 1.3 80.3 - - + +
26B ILE* 1.3 57.2 + - - +
28B GLN* 3.6 10.8 - - - +
29B LEU* 2.8 30.0 + - - +
111B ALA* 3.8 22.1 - - + +
112B LYS 5.6 0.2 - - - +
115B THR* 4.5 10.2 - - + +
116B LYS* 4.1 39.8 + - + +
119B MET* 4.1 23.6 - - + +
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Residues in contact with ILE 26 (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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22B PHE* 3.7 25.4 - - + -
23B GLN* 3.1 11.8 + - + +
25B GLU* 1.3 75.5 - - - +
27B ALA* 1.3 61.0 + - - +
29B LEU* 3.3 8.3 + - + +
30B MET* 2.9 30.6 + - + +
108B GLY* 4.0 16.6 - - - +
110B ILE 4.5 7.9 - - - +
111B ALA* 4.1 28.3 - - + -
115B THR* 4.4 12.8 - - + -
136B VAL* 4.5 10.8 - - + -
139B TYR* 3.7 39.0 - - + +
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Residues in contact with ALA 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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22B PHE* 4.0 17.4 - - + +
23B GLN 3.0 13.1 + - - +
24B ALA* 3.2 12.1 + - - +
26B ILE* 1.3 77.9 - - - +
28B GLN* 1.3 64.1 + - + +
30B MET* 3.4 8.6 + - - +
31B SER* 3.1 22.9 + - - -
168B GLY* 4.9 13.5 - - - +
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Residues in contact with GLN 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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24B ALA* 3.0 27.8 + - - +
25B GLU* 3.6 11.4 + - - +
27B ALA* 1.3 75.2 - - + +
29B LEU* 1.3 64.0 + - - +
31B SER* 3.2 7.5 + - - -
32B LEU* 3.0 30.3 + - + +
119B MET* 3.5 33.4 - - - +
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Residues in contact with LEU 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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25B GLU 2.8 17.9 + - - +
26B ILE* 3.5 12.8 - - + +
28B GLN* 1.3 76.5 - - - +
30B MET* 1.3 61.5 + - - +
32B LEU* 3.3 5.0 + - - +
33B ILE* 3.0 39.8 + - + +
115B THR* 5.3 5.6 - - + -
118B PHE* 4.0 16.6 - - + -
119B MET* 4.0 15.8 - - + +
122B LEU* 3.5 31.6 - - + -
136B VAL* 3.9 34.3 - - + +
139B TYR* 4.2 21.5 - - + -
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Residues in contact with MET 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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22B PHE* 3.5 47.3 - - + -
26B ILE* 2.9 20.5 + - + +
27B ALA* 3.8 5.8 - - - +
28B GLN 3.3 0.2 - - - -
29B LEU* 1.3 77.4 - - + +
31B SER* 1.3 62.6 + - - +
33B ILE* 3.3 7.7 + - - +
34B ILE* 3.0 31.6 + - + +
139B TYR* 3.7 26.2 - - + -
142B TYR* 3.7 32.5 - - + +
164B SER* 4.0 0.2 - - - +
166B ALA* 3.5 37.7 - - + -
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Residues in contact with SER 31 (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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27B ALA 3.1 14.1 + - - -
28B GLN* 3.5 11.0 - - - -
29B LEU 3.2 0.4 - - - -
30B MET* 1.3 75.5 - - - +
32B LEU* 1.3 66.3 + - - +
34B ILE* 3.5 2.9 + - - -
35B ASN* 3.0 45.0 + - - +
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Residues in contact with LEU 32 (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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28B GLN* 3.0 19.9 + - + +
29B LEU* 3.7 7.9 - - - +
31B SER* 1.3 76.4 - - - +
33B ILE* 1.3 57.6 + - - +
35B ASN* 5.1 0.9 - - - -
36B THR* 2.7 46.9 + - - +
38B TYR* 4.3 4.2 + - - +
119B MET* 3.6 42.2 - - + +
122B LEU* 4.1 20.6 - - + -
123B GLN* 3.2 37.9 - - - +
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Residues in contact with ILE 33 (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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29B LEU* 3.0 31.6 + - + +
30B MET* 3.7 6.1 - - - +
32B LEU* 1.3 77.7 - - - +
34B ILE* 1.3 61.7 + - - +
36B THR 3.8 7.8 - - - +
38B TYR* 4.7 4.5 - - + -
122B LEU* 5.1 2.0 - - + -
128B ILE* 4.2 15.3 - - + -
131B ILE* 4.0 15.5 - - + -
139B TYR* 3.4 42.6 - - + +
140B SER* 4.1 1.6 - - - +
142B TYR* 3.8 5.4 - - + +
143B LEU* 3.6 52.3 - - + +
191B LYS* 4.8 0.5 + - - -
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Residues in contact with ILE 34 (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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30B MET 3.0 20.4 + - - +
31B SER* 4.0 4.7 - - - +
33B ILE* 1.3 76.3 - - - +
35B ASN* 1.3 73.5 + - - +
36B THR 3.9 0.7 + - - +
142B TYR* 3.8 29.6 - - + +
145B ALA 5.4 0.9 - - - +
146B GLU* 5.7 2.7 - - - +
165B SER 4.8 2.7 - - - +
166B ALA* 3.2 37.5 - - + +
191B LYS* 3.4 29.3 + - - +
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Residues in contact with ASN 35 (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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31B SER* 3.0 39.3 + - - +
32B LEU* 4.5 0.7 - - - +
34B ILE* 1.3 91.2 - - - +
36B THR* 1.3 63.2 + - - +
37B PHE 4.2 0.5 + - - -
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Residues in contact with THR 36 (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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32B LEU* 2.7 36.1 + - - +
33B ILE 3.8 6.9 - - - +
34B ILE 3.6 1.3 - - - +
35B ASN* 1.3 82.5 - - - +
37B PHE* 1.3 71.6 + - - +
38B TYR* 3.4 40.7 + - + +
41B LYS* 4.6 6.6 + - - -
122B LEU 5.9 2.2 - - - +
143B LEU* 4.8 0.3 - - - +
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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