Contacts of the helix formed by residues 36 - 53 (chain C) in PDB entry 3CLS
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 ASN 36 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LYS* 2.9 18.3 + - + +
10C THR* 3.6 16.6 - - + -
34C ASP 3.4 1.8 + - - -
35C LEU* 1.3 74.5 - - - +
37C GLU* 1.3 75.1 + - - +
38C TRP* 3.6 15.0 - - - +
39C ASP* 2.9 32.3 + - - +
40C ASP* 3.6 3.6 + - - -
121C GLN 2.9 22.2 + - - -
122C SER* 3.5 10.8 - - - +
123C SER* 2.9 27.0 + - - -
1262C AMP 3.0 23.6 + - - -
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Residues in contact with GLU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU 3.3 4.3 + - - -
36C ASN* 1.3 76.2 + - - +
38C TRP* 1.3 77.5 + - + +
40C ASP* 3.1 26.5 + - - +
41C PHE* 3.4 22.2 - - + -
123C SER* 5.0 6.7 + - - -
184C LEU* 3.9 28.7 - - + +
210D ARG* 3.0 38.4 + - - -
237D PRO* 5.7 0.2 - - - +
1319D FAD 4.3 6.4 + - - -
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Residues in contact with TRP 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ASN* 3.2 18.7 + - - +
37C GLU* 1.3 90.2 - - + +
39C ASP* 1.3 59.1 + - - +
41C PHE* 3.2 8.3 + - - +
42C SER* 3.1 25.3 + - - -
119C GLY* 3.7 14.6 - - - -
120C VAL* 3.7 11.1 - - - +
121C GLN* 3.1 43.3 - - + -
123C SER* 4.1 23.3 - - - -
182C ILE 3.3 24.0 - - - +
183C GLN* 2.8 23.1 + - - -
184C LEU* 3.4 37.6 - - + +
1319D FAD 3.6 35.7 - - + -
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Residues in contact with ASP 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ALA 3.4 10.6 - - - +
7C VAL* 3.3 24.2 - - + +
8C LYS 2.8 27.4 + - - +
35C LEU* 4.0 12.2 - - + +
36C ASN* 2.9 25.2 + - - +
38C TRP* 1.3 76.4 - - - +
40C ASP* 1.3 60.3 + - - +
42C SER* 2.9 7.0 + - - -
43C LEU* 2.9 32.9 + - - +
119C GLY 3.8 5.2 + - - -
1262C AMP 2.5 26.2 + - - -
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Residues in contact with ASP 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU* 3.3 23.8 - - - +
36C ASN 3.6 4.4 + - - -
37C GLU* 3.1 24.9 + - - +
39C ASP* 1.3 78.6 - - - +
41C PHE* 1.3 60.0 + - + +
43C LEU* 4.0 4.1 - - - +
44C GLU* 3.0 29.6 + - - +
79C LYS* 4.3 17.3 + - - +
189C PRO* 3.7 21.3 - - + +
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Residues in contact with PHE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C GLU* 3.4 29.6 - - + -
38C TRP 3.2 7.2 + - - +
40C ASP* 1.3 76.8 - - + +
42C SER* 1.3 59.0 + - - +
45C GLU* 2.9 13.5 + - - +
182C ILE* 4.2 4.5 - - + -
183C GLN 4.2 5.8 - - - +
184C LEU* 3.5 30.3 - - + -
185C GLY* 3.4 24.2 - - - -
186C ILE* 3.9 12.3 - - + +
187C ASN* 2.9 55.8 + - - -
189C PRO* 3.2 25.4 - - + -
210D ARG* 6.3 0.7 - - - -
240D ASP* 5.5 3.1 - - + -
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Residues in contact with SER 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 3.4 21.0 - - - +
38C TRP 3.1 10.2 + - - -
39C ASP* 2.9 24.4 + - - -
41C PHE* 1.3 74.6 - - - +
43C LEU* 1.3 71.8 + - - +
45C GLU* 3.1 5.7 + - - +
46C ALA* 3.0 19.1 + - - +
117C PHE* 3.7 14.1 - - - -
118C ALA 4.6 10.1 - - - -
182C ILE* 4.0 29.7 - - - +
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 4.3 10.3 - - + -
7C VAL* 5.6 1.6 - - + -
35C LEU* 5.6 3.6 - - + -
39C ASP 2.9 15.7 + - - +
40C ASP* 4.0 4.3 - - - +
42C SER* 1.3 83.5 + - - +
44C GLU* 1.3 62.1 + - - +
46C ALA* 3.2 3.7 + - - +
47C MET* 3.0 35.7 + - + +
59C VAL* 3.9 26.7 - - + -
61C VAL* 4.0 17.0 - - + -
76C CYS* 4.0 40.2 - - + +
79C LYS* 4.7 18.8 - - + -
81C ALA* 4.3 6.5 - - + +
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Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ASP 3.0 20.0 + - - +
42C SER 3.3 0.2 - - - -
43C LEU* 1.3 76.3 - - - +
45C GLU* 1.3 57.9 + - - +
47C MET* 3.2 11.7 + - - +
48C LYS* 2.7 47.5 + - + +
187C ASN* 3.4 32.8 - - + +
188C LYS 4.2 4.5 - - - +
189C PRO* 3.9 10.5 - - + +
190C ARG* 3.1 36.0 + - - +
191C TYR* 5.1 5.2 - - - -
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Residues in contact with GLU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C PHE 2.9 15.0 + - - +
42C SER* 3.1 10.1 + - - +
44C GLU* 1.3 75.9 - - - +
46C ALA* 1.3 61.1 + - - +
48C LYS* 3.3 16.2 + - - +
49C ILE* 3.1 30.4 + - + +
117C PHE* 4.0 16.2 - - + -
149C LEU* 3.8 34.4 + - + +
182C ILE* 5.0 3.1 - - + -
186C ILE* 3.7 32.4 - - + +
187C ASN* 2.9 25.9 + - - +
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Residues in contact with ALA 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ILE* 3.9 22.2 - - + +
5C VAL* 3.8 28.0 - - + -
42C SER 3.0 7.3 + - - +
43C LEU 3.6 7.0 - - - +
45C GLU* 1.3 75.8 - - - +
47C MET* 1.3 58.4 + - - +
49C ILE* 3.3 4.5 + - - +
50C LYS* 2.9 26.3 + - - +
59C VAL* 3.9 20.6 - - + +
117C PHE* 3.7 7.5 - - + -
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Residues in contact with MET 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LEU* 3.0 24.2 + - + +
44C GLU* 3.6 16.2 - - - +
46C ALA* 1.3 74.8 - - - +
48C LYS* 1.3 59.4 + - - +
50C LYS* 3.3 20.6 + - + +
51C GLU* 2.8 31.2 + - - +
59C VAL* 4.1 23.8 - - - -
79C LYS 3.9 10.8 - - - +
80C GLY* 3.4 43.7 - - - +
81C ALA* 4.1 2.9 - - - -
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Residues in contact with LYS 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C GLU* 2.7 38.6 + - - +
45C GLU* 3.3 19.1 + - - +
47C MET* 1.3 73.0 - - - +
49C ILE* 1.3 63.0 + - + +
51C GLU* 3.3 7.2 + - - +
52C SER* 3.0 26.0 + - - -
186C ILE 4.6 3.8 + - - -
187C ASN* 3.7 36.3 - - + +
188C LYS 5.1 1.6 - - - +
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Residues in contact with ILE 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 5.0 0.2 - - + -
3C ILE* 3.7 28.7 - - + -
45C GLU* 3.1 19.7 + - + +
46C ALA 3.6 5.8 - - - +
48C LYS* 1.3 76.5 - - + +
50C LYS* 1.3 63.2 + - - +
52C SER* 3.4 6.3 + - - -
53C SER* 3.3 22.5 + - - -
57C VAL* 4.6 3.8 - - + -
117C PHE* 3.8 19.5 - - + -
149C LEU* 4.1 15.7 - - + -
151C TYR* 4.2 24.7 - - + +
153C PRO* 4.0 28.5 - - + +
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Residues in contact with LYS 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ALA 2.9 14.8 + - - +
47C MET* 3.5 34.3 - - + +
49C ILE* 1.3 78.1 - - - +
51C GLU* 1.3 60.6 + - - +
52C SER 3.5 0.2 + - - -
53C SER* 3.5 17.3 + - - +
55C THR 4.8 1.4 - - - +
57C VAL* 2.7 50.8 + - + +
59C VAL* 4.3 2.7 - - + -
80C GLY 4.5 6.3 - - - -
82C ASP* 2.8 32.5 + - - +
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Residues in contact with GLU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C MET 2.8 20.0 + - - +
48C LYS* 3.8 6.7 - - - +
50C LYS* 1.3 74.7 - - - +
52C SER* 1.3 62.5 + - - +
53C SER 3.4 3.6 + - - +
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Residues in contact with SER 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LYS 3.0 18.5 + - - -
49C ILE* 3.4 6.5 + - - -
51C GLU* 1.3 77.3 - - - +
53C SER* 1.3 58.5 + - - +
54C ASP 4.1 0.7 + - - -
153C PRO* 6.3 0.2 - - - -
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Residues in contact with SER 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE 3.3 15.4 + - - -
50C LYS 3.6 10.8 - - - +
51C GLU 3.2 4.2 - - - +
52C SER* 1.3 78.4 - - - +
54C ASP* 1.3 60.6 + - - +
55C THR* 2.8 45.7 + - - +
57C VAL* 3.9 3.8 - - - +
153C PRO* 3.6 23.8 - - - +
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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
------------------------------------------------------------
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