Contacts of the helix formed by residues 23 - 36 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ALA 3.6 1.4 + - - -
22A PHE* 1.3 74.8 - - - +
24A ALA* 1.3 82.1 + - - +
25A GLU* 2.9 39.8 + - - +
26A ILE* 3.0 8.7 + - + +
27A ALA* 3.0 15.9 + - - +
108A GLY 2.8 19.6 + - - +
109A THR* 3.6 21.0 - - - +
111A ALA* 2.9 34.9 - - + +
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Residues in contact with ALA 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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22A PHE 3.6 3.4 + - - -
23A GLN* 1.3 83.0 - - - +
25A GLU* 1.3 59.5 + - + +
27A ALA* 3.2 9.5 + - - +
28A GLN* 3.0 42.2 + - - +
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Residues in contact with GLU 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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23A GLN* 2.9 29.0 + - - +
24A ALA* 1.3 74.8 - - + +
26A ILE* 1.3 58.2 + - - +
28A GLN* 3.2 19.8 + - - +
29A LEU 2.9 23.4 + - - -
111A ALA* 3.8 9.5 - - - +
112A LYS 4.8 4.0 - - - +
115A THR* 3.5 17.9 - - + +
116A LYS* 3.9 34.2 + - + +
119A MET* 3.4 14.5 - - + +
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Residues in contact with ILE 26 (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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22A PHE* 3.8 17.7 - - + -
23A GLN* 3.0 8.8 + - + +
25A GLU* 1.3 74.9 - - - +
27A ALA* 1.3 65.4 + - - +
29A LEU* 3.3 3.7 + - + +
30A MET* 3.0 24.0 + - + +
106A ASN 6.0 0.7 - - - +
108A GLY* 3.5 28.7 - - - +
110A ILE 4.0 18.2 - - - +
111A ALA* 4.1 19.5 - - + -
112A LYS 5.6 0.2 - - - +
115A THR* 4.0 17.0 - - + +
139A TYR* 3.6 44.4 - - + +
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Residues in contact with ALA 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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22A PHE* 4.1 18.3 - - + +
23A GLN 3.0 11.2 + - - +
24A ALA* 3.4 12.3 - - - +
26A ILE* 1.3 78.0 - - - +
28A GLN* 1.3 61.0 + - + +
30A MET* 3.4 9.0 + - - +
31A SER* 3.1 22.9 + - - -
168A GLY* 4.7 13.9 - - - +
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Residues in contact with GLN 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 ALA* 3.0 35.7 + - - +
25A GLU* 3.4 19.2 - - - +
26A ILE 3.2 0.2 - - - -
27A ALA* 1.3 77.6 - - + +
29A LEU* 1.3 61.7 + - - +
31A SER* 3.3 7.8 + - - -
32A LEU* 3.0 23.0 + - - +
119A MET* 3.7 21.9 - - - +
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Residues in contact with LEU 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 GLU 2.9 16.6 + - - +
26A ILE* 3.6 6.7 - - - +
28A GLN* 1.3 76.6 - - - +
30A MET* 1.3 57.7 + - - +
32A LEU* 3.3 8.4 + - + +
33A ILE* 3.0 46.9 + - + +
115A THR* 4.3 15.9 - - + +
118A PHE* 3.6 26.9 - - + -
119A MET* 3.6 21.7 - - + -
131A ILE* 5.0 0.2 - - + -
136A VAL* 4.0 32.5 - - + -
139A TYR* 4.2 21.1 - - + -
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Residues in contact with MET 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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22A PHE* 3.4 49.4 - - + -
26A ILE 3.0 21.5 + - - +
27A ALA* 3.8 5.8 - - - +
29A LEU* 1.3 76.9 - - - +
31A SER* 1.3 57.3 - - - +
33A ILE* 3.9 5.5 - - - +
34A ILE* 3.0 35.3 + - - +
139A TYR* 3.7 26.7 - - + -
142A TYR* 3.5 41.9 - - + +
162A TRP* 5.2 0.2 - - + -
164A SER* 4.0 0.2 - - - +
166A ALA* 3.7 28.9 - - + +
168A GLY 6.1 0.2 - - - -
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Residues in contact with SER 31 (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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27A ALA 3.1 14.3 + - - -
28A GLN* 3.6 10.8 - - - -
30A MET* 1.3 74.7 - - - +
32A LEU* 1.3 64.2 + - - +
34A ILE* 4.1 3.4 - - - -
35A ASN* 2.9 47.8 + - - +
166A ALA 5.9 1.8 + - - -
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Residues in contact with LEU 32 (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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28A GLN 3.0 12.9 + - - +
29A LEU* 3.5 11.4 - - + +
31A SER* 1.3 76.6 - - - +
33A ILE* 1.3 62.5 + - + +
36A THR* 2.7 49.7 + - + +
38A TYR* 3.7 10.5 - - - +
119A MET* 4.5 22.0 - - + +
122A LEU* 3.8 32.3 - - + -
123A GLN* 6.0 5.6 - - - +
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Residues in contact with ILE 33 (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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29A LEU* 3.0 46.0 + - + +
30A MET* 3.9 4.5 - - - +
32A LEU* 1.3 80.5 - - + +
34A ILE* 1.3 62.4 + - - +
35A ASN 3.3 0.9 + - - -
36A THR 3.8 12.1 + - - +
38A TYR* 4.1 6.9 - - - +
41A LYS* 6.0 0.2 - - - -
118A PHE* 5.1 0.4 - - + -
128A ILE* 4.2 14.8 - - + -
131A ILE* 4.0 17.0 - - + -
139A TYR* 3.6 36.8 - - + +
140A SER* 4.2 1.3 - - - +
142A TYR* 3.8 4.4 - - + +
143A LEU* 3.7 41.7 - - + +
191A LYS* 4.8 0.7 + - - -
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Residues in contact with ILE 34 (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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30A MET 3.0 22.4 + - - +
31A SER* 3.7 9.2 - - - +
33A ILE* 1.3 77.1 - - - +
35A ASN* 1.3 76.9 + - - +
36A THR 5.1 0.2 - - - -
142A TYR* 3.4 44.0 - - + +
145A ALA 4.1 5.6 - - - +
146A GLU* 4.5 10.8 - - + +
165A SER 4.5 6.3 - - - +
166A ALA* 4.1 17.5 - - + +
191A LYS* 2.9 31.0 + - - +
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Residues in contact with ASN 35 (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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31A SER* 2.9 37.7 + - - +
32A LEU 4.4 0.4 - - - +
33A ILE 3.2 0.2 - - - -
34A ILE* 1.3 94.0 - - - +
36A THR* 1.3 62.9 + - - +
37A PHE 3.9 1.0 + - - -
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Residues in contact with THR 36 (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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32A LEU* 2.7 39.9 + - + +
33A ILE 3.8 4.5 + - - +
34A ILE 3.7 0.5 - - - -
35A ASN* 1.3 82.0 - - - +
37A PHE* 1.3 76.9 + - - +
38A TYR* 3.2 37.7 + - + +
41A LYS* 4.4 9.0 + - - -
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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