Contacts of the helix formed by residues 2 - 14 (chain C) in PDB entry 5BMU
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 ALA 2 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0C HIS 3.8 3.4 + - - +
1C MET* 1.3 75.0 - - - +
3C ALA* 1.3 60.3 + - - +
4C ALA* 4.2 5.4 - - + +
5C ALA* 3.2 20.3 + - + +
6C GLU* 2.9 26.2 + - - +
29C GLN* 5.8 5.4 - - + +
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Residues in contact with ALA 3 (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 3.6 2.7 + - - -
2C ALA* 1.3 73.7 - - - +
4C ALA* 1.3 61.7 + - - +
6C GLU* 3.4 8.2 + - - +
7C LEU* 3.2 28.2 + - - +
29C GLN 4.3 11.7 + - - +
30C ILE* 5.3 0.2 - - - -
31C PRO* 3.5 33.4 - - + -
44C LEU* 4.2 14.6 - - + +
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Residues in contact with ALA 4 (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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2C ALA* 3.1 6.2 - - + +
3C ALA* 1.3 79.4 - - - +
5C ALA* 1.3 60.3 + - - +
7C LEU* 3.4 8.2 + - - +
8C SER* 3.3 23.6 + - - -
22C TYR* 3.8 32.9 - - + +
23C SER 4.4 12.6 - - - +
24C ALA* 5.3 6.1 - - + -
29C GLN 5.7 0.4 + - - -
31C PRO* 4.3 3.0 - - + +
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Residues in contact with ALA 5 (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* 4.3 16.6 - - + +
2C ALA* 3.4 25.2 - - + +
4C ALA* 1.3 80.6 - - - +
6C GLU* 1.3 60.2 + - - +
8C SER* 3.2 17.1 + - - -
9C LEU* 3.3 12.0 + - - +
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Residues in contact with GLU 6 (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* 4.3 24.2 - - + +
2C ALA 2.9 16.2 + - - +
3C ALA* 3.7 8.1 - - - +
4C ALA 3.4 0.2 - - - -
5C ALA* 1.3 73.1 - - - +
7C LEU* 1.3 60.5 + - - +
9C LEU* 3.2 10.3 + - + +
10C LEU* 3.0 25.7 + - + +
44C LEU* 3.5 21.3 - - + +
78C ARG* 2.3 38.0 + - - -
119C LEU* 4.3 9.2 - - + +
122C TYR* 3.7 35.0 - - + +
123C GLY* 4.5 0.3 - - - -
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Residues in contact with LEU 7 (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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3C ALA 3.2 17.2 + - - +
4C ALA 3.6 6.5 - - - +
5C ALA 3.2 0.2 - - - -
6C GLU* 1.3 73.8 - - - +
8C SER* 1.3 65.7 + - - +
10C LEU* 3.1 14.1 + - + +
11C GLU* 3.0 23.9 + - - +
22C TYR* 3.8 25.1 - - + -
31C PRO* 3.8 27.4 - - + -
44C LEU* 4.0 26.7 - - + +
47C ILE* 3.6 34.8 - - + -
48C ALA 4.2 3.6 - - - +
51C LEU* 3.8 13.3 - - + +
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Residues in contact with SER 8 (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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4C ALA 3.3 11.2 + - - -
5C ALA* 3.2 11.5 + - - -
7C LEU* 1.3 77.4 - - - +
9C LEU* 1.3 62.7 + - - +
11C GLU* 3.1 26.6 + - - +
12C LYS* 3.2 28.5 + - - +
20C ASN 5.1 2.6 + - - -
22C TYR* 4.1 10.6 - - - -
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Residues in contact with LEU 9 (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* 3.9 21.8 - - + -
5C ALA 3.3 9.0 + - - +
6C GLU* 3.2 9.2 + - - +
7C LEU 3.2 0.2 - - - -
8C SER* 1.3 79.3 - - - +
10C LEU* 1.3 57.4 + - - +
12C LYS* 3.3 11.8 + - - +
13C SER* 2.8 23.6 + - - -
122C TYR* 3.5 44.6 - - + +
156C ARG 4.0 7.9 - - - +
157C GLN* 3.3 36.6 - - + +
158C HIS* 4.0 20.4 - - + +
159C LEU* 3.8 12.3 - - + -
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Residues in contact with LEU 10 (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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6C GLU* 3.0 13.1 + - + +
7C LEU* 3.1 12.3 + - + +
9C LEU* 1.3 74.8 - - - +
11C GLU* 1.3 63.1 - - - +
12C LYS 3.1 2.0 - - - -
13C SER* 3.2 10.9 + - - -
14C LEU* 3.2 41.1 + - + +
44C LEU* 6.2 0.2 - - + -
48C ALA* 3.5 37.7 - - + +
51C LEU* 4.3 10.5 - - + -
115C LEU* 4.2 7.9 - - + -
118C ILE* 3.9 35.0 - - + -
119C LEU* 4.1 9.6 - - + -
122C TYR* 4.3 7.0 - - + -
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Residues in contact with GLU 11 (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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7C LEU 3.0 7.7 + - - +
8C SER* 3.1 19.4 + - - +
10C LEU* 1.3 76.3 - - - +
12C LYS* 1.3 64.8 + - + +
14C LEU* 3.8 1.7 + - - +
15C GLY 3.7 1.6 + - - -
16C LEU* 3.0 50.1 + - + +
18C LYS 3.5 22.7 - - - +
19C GLY* 3.6 11.3 - - - -
20C ASN* 3.5 19.3 + - - +
22C TYR* 2.5 31.6 + - - -
51C LEU* 3.7 18.1 - - + +
54C GLN* 5.3 0.2 - - - +
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Residues in contact with LYS 12 (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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8C SER* 3.2 24.0 + - - +
9C LEU* 3.6 9.2 - - - +
10C LEU 3.1 0.6 - - - -
11C GLU* 1.3 84.5 - - + +
13C SER* 1.3 56.1 + - - +
15C GLY* 3.0 19.3 + - - +
16C LEU 4.7 7.4 - - - +
154C GLY* 5.6 0.5 - - - -
157C GLN* 3.4 32.7 + - + +
158C HIS* 5.9 6.7 - - + -
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Residues in contact with SER 13 (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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9C LEU 2.8 12.2 + - - -
10C LEU* 3.2 17.0 + - - -
12C LYS* 1.3 75.7 - - - +
14C LEU* 1.3 59.0 + - - +
15C GLY 3.3 1.8 + - - -
57C LYS* 4.8 3.8 + - - -
118C ILE* 4.9 1.6 - - - -
122C TYR* 2.3 32.0 + - - -
153C PRO 4.5 5.7 - - - +
154C GLY* 3.6 19.9 + - - +
155C ILE* 3.6 25.2 + - - +
157C GLN* 3.9 1.2 - - - +
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Residues in contact with LEU 14 (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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10C LEU* 3.2 42.6 + - + +
11C GLU 4.2 4.0 - - - +
12C LYS 3.2 0.4 - - - -
13C SER* 1.3 75.7 - - - +
15C GLY* 1.3 60.1 + - - +
16C LEU* 3.4 4.0 + - + +
51C LEU* 3.7 13.5 - - + +
52C VAL* 3.5 38.6 - - + +
55C ALA* 3.7 17.5 - - + +
57C LYS* 3.5 30.1 - - + +
60C LEU* 3.7 29.8 - - + -
118C ILE* 4.2 10.1 - - + -
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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