Contacts of the helix formed by residues 25 - 36 (chain B) in PDB entry 2CLS
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 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B GLN 3.3 3.0 - - - -
24B CYS* 1.3 79.3 - - - +
26B LYS* 1.3 65.2 + - - +
28B ALA* 3.6 2.9 + - - +
29B MET* 3.2 27.5 + - - +
125B CYS* 4.3 11.1 - - - +
126B LYS* 4.3 0.7 - - - -
169B ALA* 5.3 0.2 - - - +
500B GTP 3.1 36.4 + - - -
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Residues in contact with LYS 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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18B LEU* 3.7 16.5 - - + +
19B VAL* 3.5 34.5 - - - +
20B GLY 3.0 23.6 + - - +
21B ASP 3.1 7.7 + - - -
24B CYS* 3.7 11.1 - - - -
25B GLY* 1.3 76.1 - - - +
27B THR* 1.3 63.8 + - - +
29B MET* 3.4 9.8 + - - +
30B LEU* 3.2 24.6 + - - +
67B ASP* 3.8 10.8 - - - +
68B THR* 3.2 27.6 - - - -
70B GLY 4.3 0.9 - - - +
91B CYS* 3.9 15.0 - - + -
500B GTP 2.8 44.5 + - - +
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Residues in contact with THR 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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26B LYS* 1.3 72.3 - - - +
28B ALA* 1.3 61.2 + - - +
30B LEU* 3.2 2.2 + - - +
31B GLN* 2.9 45.2 + - + +
39B PRO* 4.9 5.2 - - + -
43B VAL 5.5 4.3 - - - +
45B THR* 2.8 4.0 + - - +
48B GLU* 6.5 0.4 - - + -
50B TYR* 4.0 8.7 - - - +
67B ASP* 2.6 25.1 + - - +
500B GTP 3.0 15.8 + - - +
550B MG 1.9 32.4 - - - -
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Residues in contact with ALA 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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25B GLY 3.8 2.7 - - - +
27B THR* 1.3 74.0 - - - +
29B MET* 1.3 61.4 + - - +
31B GLN* 3.9 0.9 - - - +
32B VAL* 3.1 29.6 + - - +
37B CYS 4.3 0.2 - - - +
38B TYR* 4.1 2.0 - - + -
39B PRO* 3.7 27.0 - - + +
169B ALA* 3.9 7.0 - - + -
500B GTP 2.7 54.1 + - + +
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Residues in contact with MET 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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18B LEU* 3.8 15.3 - - + -
25B GLY 3.2 15.5 + - - +
26B LYS* 3.6 5.2 - - - +
27B THR 3.2 0.4 - - - -
28B ALA* 1.3 79.2 - - - +
30B LEU* 1.3 58.3 + - - +
32B VAL* 3.3 1.4 + - - +
33B LEU* 2.9 29.2 + - - +
89B LEU* 5.7 0.7 - - + -
91B CYS* 3.8 30.1 - - - -
123B ILE* 3.9 20.9 - - + -
124B GLY 5.4 0.4 - - - +
125B CYS* 3.8 20.9 - - + -
167B GLY 6.4 0.2 - - - -
169B ALA* 4.1 9.9 - - + +
176B ILE* 3.5 27.8 - - + +
179B ILE* 4.1 16.6 - - - -
180B PHE* 4.5 15.3 - - + -
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Residues in contact with LEU 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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18B LEU* 3.9 26.0 - - + -
26B LYS 3.2 9.3 + - - +
27B THR* 3.2 7.6 + - - +
29B MET* 1.3 73.4 - - - +
31B GLN* 1.3 60.6 + - - +
33B LEU* 3.8 4.2 - - + +
34B ALA* 2.8 35.2 + - - +
50B TYR* 3.8 27.1 - - + -
65B LEU* 4.2 22.7 - - + -
67B ASP* 3.7 37.5 - - + +
180B PHE* 3.7 31.9 - - + -
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Residues in contact with GLN 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 THR* 2.9 32.1 + - + +
28B ALA 3.9 3.1 - - - +
30B LEU* 1.3 75.7 - - - +
32B VAL* 1.3 58.2 + - - +
35B LYS* 3.0 37.1 + - - +
37B CYS* 2.9 43.7 + - - +
39B PRO* 4.2 16.1 - - + -
50B TYR* 2.7 34.7 + - - +
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Residues in contact with VAL 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 ALA 3.1 18.5 + - - +
29B MET* 3.6 4.0 - - - +
31B GLN* 1.3 75.5 - - - +
33B LEU* 1.3 66.7 + - - +
36B ASP* 3.1 15.2 + - - -
37B CYS 2.9 23.6 + - - +
38B TYR* 4.2 9.2 - - + -
169B ALA* 3.7 25.1 - - + +
173B GLU* 3.1 52.6 - - + +
176B ILE* 4.1 15.7 - - + -
177B HIS* 4.1 0.7 + - - -
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Residues in contact with LEU 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 MET 2.9 18.3 + - - +
30B LEU* 3.8 5.6 - - + +
32B VAL* 1.3 80.7 - - - +
34B ALA* 1.3 60.3 + - - +
36B ASP 4.6 0.7 + - - -
52B ALA* 3.9 13.7 - - + +
54B LEU* 4.5 7.6 - - + -
63B LEU* 4.5 2.2 - - + -
65B LEU* 3.7 31.2 - - + -
176B ILE* 4.2 7.6 - - + +
177B HIS* 3.5 53.4 - - + +
180B PHE* 3.8 45.1 - - + -
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Residues in contact with ALA 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 LEU 2.8 17.9 + - - +
33B LEU* 1.3 76.6 - - + +
35B LYS* 1.3 70.1 + - + +
36B ASP 3.8 0.2 - - - -
50B TYR* 3.9 31.9 - - + -
51B THR 4.3 15.0 - - - +
52B ALA* 4.6 11.2 - - + -
65B LEU* 5.0 1.8 - - + -
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Residues in contact with LYS 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 GLN* 3.0 32.0 + - - +
34B ALA* 1.3 89.9 + - + +
36B ASP* 1.3 72.0 + - - +
37B CYS* 3.1 20.6 + - + +
50B TYR* 4.1 24.5 - - + -
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Residues in contact with ASP 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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31B GLN 3.1 2.2 + - - -
32B VAL* 3.1 17.3 + - - -
33B LEU 4.6 0.6 + - - -
34B ALA 3.8 0.8 - - - -
35B LYS* 1.3 79.5 - - - +
37B CYS* 1.3 59.3 + - - +
173B GLU* 2.8 33.3 - - - +
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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