Contacts of the helix formed by residues 35 - 49 (chain A) in PDB entry 1CL8
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 VAL 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ALA* 1.3 73.6 - - + +
36A GLY* 1.3 63.5 + - - +
38A VAL* 3.4 8.5 + - - +
39A SER* 3.1 25.8 + - - -
91A ASP* 3.7 25.4 - - - +
92A GLY* 3.9 4.9 - - - -
110A ALA* 3.7 26.9 - - + -
111A GLU 4.3 3.6 - - - +
112A ALA* 3.9 25.8 - - + -
168A PHE* 4.3 13.0 - - + -
251A MET* 4.4 12.1 - - - +
255A MET* 4.0 14.0 - - + +
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Residues in contact with GLY 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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34A ALA* 3.1 3.8 - - - +
35A VAL* 1.3 84.5 - - - +
37A GLU* 1.3 64.5 + - - +
39A SER* 3.3 12.6 + - - -
40A LYS* 3.4 17.3 + - - +
57A TYR* 3.7 9.5 + - - -
91A ASP 3.5 18.7 + - - -
92A GLY 3.7 9.4 - - - -
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Residues in contact with GLU 37 (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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33A LEU* 4.0 30.4 - - + +
34A ALA* 3.0 21.3 + - + +
36A GLY* 1.3 74.9 - - - +
38A VAL* 1.3 61.0 + - - +
39A SER 3.3 0.2 - - - -
40A LYS* 3.2 40.6 + - - +
41A LEU* 3.1 24.1 + - - +
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Residues in contact with VAL 38 (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 ALA* 5.0 1.3 - - + -
33A LEU* 3.8 25.4 - - + +
34A ALA 2.9 21.6 + - - +
35A VAL 3.7 7.0 - - - +
36A GLY 3.2 0.2 - - - -
37A GLU* 1.3 74.9 - - - +
39A SER* 1.3 60.1 + - - +
41A LEU* 3.1 8.3 + - + +
42A VAL* 2.8 27.6 + - + +
248A SER* 4.6 7.9 - - - +
251A MET* 4.1 13.0 - - + -
252A PHE* 3.6 34.8 - - + +
255A MET* 3.5 24.2 - - + -
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Residues in contact with SER 39 (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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35A VAL 3.1 11.9 + - - -
36A GLY 3.5 5.2 - - - -
37A GLU 3.3 0.2 - - - -
38A VAL* 1.3 78.4 - - - +
40A LYS* 1.3 60.4 + - - +
42A VAL* 3.4 10.2 + - - +
43A LYS* 3.2 18.4 + - - +
57A TYR* 3.6 11.4 - - - -
92A GLY 2.7 29.2 + - - -
93A GLY* 5.3 0.9 - - - -
95A VAL* 3.7 19.0 - - - +
108A LEU* 4.4 4.9 - - - +
110A ALA* 3.7 15.9 + - - +
255A MET* 4.1 4.2 - - - -
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Residues in contact with LYS 40 (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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36A GLY 3.4 9.4 + - - +
37A GLU* 3.2 42.4 + - - +
38A VAL 3.2 0.2 - - - -
39A SER* 1.3 76.4 - - - +
41A LEU* 1.3 63.1 + - - +
43A LYS* 3.4 14.5 + - + +
44A LYS* 3.1 21.8 + - - +
57A TYR* 3.5 43.5 - - + -
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Residues in contact with LEU 41 (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 PHE* 3.5 49.3 - - + +
27A TYR* 4.0 23.3 - - + -
28A ALA* 3.7 23.6 - - + +
33A LEU* 4.0 9.4 - - + -
37A GLU 3.1 14.0 + - - +
38A VAL* 3.1 12.0 + - - +
40A LYS* 1.3 77.4 - - - +
42A VAL* 1.3 58.1 + - - +
44A LYS* 3.3 8.1 + - + +
45A ALA* 3.0 26.7 + - - +
252A PHE* 3.8 15.9 - - + -
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Residues in contact with VAL 42 (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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38A VAL* 2.8 22.3 + - + +
39A SER* 3.5 10.8 - - - +
40A LYS 3.2 0.2 - - - -
41A LEU* 1.3 75.2 - - - +
43A LYS* 1.3 60.9 + - - +
45A ALA* 3.1 4.3 + - - +
46A LEU* 2.9 35.7 + - + +
95A VAL* 5.3 1.6 - - + -
108A LEU* 4.2 7.4 - - + -
252A PHE* 3.7 26.9 - - + +
255A MET* 4.0 24.0 - - + -
256A PHE* 4.1 16.2 - - + +
259A SER* 3.6 23.3 - - - +
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Residues in contact with LYS 43 (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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39A SER 3.2 8.5 + - - +
40A LYS* 3.4 16.0 + - - +
41A LEU 3.4 0.2 - - - -
42A VAL* 1.3 79.1 - - - +
44A LYS* 1.3 80.7 + - - +
46A LEU* 3.4 12.3 + - - +
47A SER* 3.1 35.0 + - - +
55A PHE* 4.1 32.0 - - + +
56A ARG* 4.2 11.4 - - - +
57A TYR* 4.5 11.7 - - + +
95A VAL* 3.7 24.7 - - + +
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Residues in contact with LYS 44 (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 PHE* 4.1 18.6 - - + -
40A LYS 3.1 13.6 + - - +
41A LEU* 3.4 15.5 - - + +
42A VAL 3.1 0.2 - - - -
43A LYS* 1.3 91.8 - - - +
45A ALA* 1.3 60.3 + - - +
47A SER* 2.9 27.3 + - - -
48A ASN* 3.3 24.1 + - - +
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Residues in contact with ALA 45 (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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20A VAL* 5.3 3.8 - - + +
21A ILE* 5.6 2.2 - - + -
24A PHE* 3.8 23.1 - - + -
41A LEU 3.0 14.1 + - - +
42A VAL 3.5 7.0 - - - +
44A LYS* 1.3 77.2 - - - +
46A LEU* 1.3 58.9 + - - +
48A ASN* 3.3 6.2 + - - +
49A GLU* 3.0 33.1 + - + +
252A PHE* 3.9 12.8 - - + -
256A PHE* 3.8 18.2 - - + -
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Residues in contact with LEU 46 (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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42A VAL* 2.9 25.7 + - + +
43A LYS* 3.7 11.2 - - - +
44A LYS 3.3 0.2 - - - -
45A ALA* 1.3 75.1 - - - +
47A SER* 1.3 58.2 + - - +
48A ASN 3.1 0.4 - - - -
49A GLU* 4.7 0.2 - - - -
50A TYR* 2.9 40.7 + - + -
55A PHE* 3.4 34.0 - - + -
95A VAL* 4.3 9.6 - - + -
107A VAL* 4.3 4.3 - - + -
256A PHE* 3.7 23.6 - - + -
259A SER* 4.0 26.9 - - - +
260A THR* 4.4 4.0 - - + -
263A LEU* 4.2 22.2 - - + -
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Residues in contact with SER 47 (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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43A LYS* 3.1 19.3 + - - -
44A LYS* 2.9 35.8 + - - -
46A LEU* 1.3 76.5 - - - +
48A ASN* 1.3 59.2 + - - +
50A TYR 3.5 13.5 - - - +
51A PRO* 3.5 13.5 - - - +
53A LEU 5.1 3.1 - - - -
55A PHE* 3.8 19.7 - - - -
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Residues in contact with ASN 48 (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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20A VAL* 3.4 35.1 - - + +
24A PHE* 4.8 8.7 - - + -
44A LYS* 3.3 24.3 + - - +
45A ALA* 3.4 12.3 - - - +
46A LEU 3.1 0.4 - - - -
47A SER* 1.3 79.9 + - - +
49A GLU* 1.3 69.8 + - - +
51A PRO* 3.6 14.8 - - - +
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Residues in contact with GLU 49 (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 GLN* 3.3 29.8 + - - +
19A GLY* 5.6 0.9 - - - -
20A VAL* 3.5 10.4 + - + +
21A ILE* 3.8 12.9 - - + +
45A ALA 3.0 20.2 + - - +
46A LEU* 4.6 0.7 - - - -
48A ASN* 1.3 93.4 + - - +
50A TYR* 1.3 86.7 + - + +
51A PRO* 3.5 6.8 - - - +
52A GLN* 4.9 0.2 - - - +
256A PHE* 4.1 17.6 - - + -
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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