Contacts of the helix formed by residues 2 - 16 (chain B) in PDB entry 4A49
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B LEU* 1.3 68.8 + - - +
4B LYS* 3.2 3.0 - - - +
5B ARG* 3.1 10.2 + - - +
6B ILE* 2.9 30.3 + - + +
31B PHE* 3.9 22.9 - - + -
57B PRO 4.4 3.6 - - - +
58B THR 3.8 18.1 + - - +
60B TYR* 3.2 30.7 + - + +
61B PRO* 5.2 1.1 - - - -
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Residues in contact with LEU 3 (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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2B ALA* 1.3 78.1 - - - +
4B LYS* 1.3 81.1 + - + +
6B ILE* 3.3 3.0 + - - -
7B HIS* 2.8 38.1 + - + +
30B MET* 3.4 38.1 - - + +
31B PHE* 4.5 7.5 - - + -
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Residues in contact with LYS 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A CYS 3.6 15.0 - - - +
385A ALA* 3.6 21.1 - - - +
386A GLU* 2.8 47.7 + - + +
2B ALA 3.2 1.6 - - - +
3B LEU* 1.3 94.5 - - + +
5B ARG* 1.3 57.9 + - - +
7B HIS* 3.5 17.3 + - + +
8B LYS* 3.1 21.1 + - - +
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Residues in contact with ARG 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A LYS 3.5 18.6 + - - -
383A ILE* 2.8 41.7 + - - +
384A CYS* 3.5 9.6 + - - +
385A ALA* 4.1 7.9 - - - -
2B ALA* 3.1 9.5 + - - +
4B LYS* 1.3 78.4 - - - +
6B ILE* 1.3 63.7 + - - +
8B LYS* 3.2 6.2 + - - +
9B GLU* 2.8 50.2 + - - +
60B TYR* 3.6 24.0 + - + -
61B PRO* 3.4 17.7 - - + +
95B PRO 2.8 25.8 + - - -
96B ALA* 3.8 6.1 + - - +
97B LEU 2.9 31.5 + - - -
98B THR* 4.3 1.8 - - - +
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Residues in contact with ILE 6 (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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2B ALA* 2.9 24.1 + - + +
3B LEU 3.8 3.4 - - - +
5B ARG* 1.3 75.0 - - - +
7B HIS* 1.3 62.9 + - - +
9B GLU* 3.3 10.2 + - - +
10B LEU* 3.1 19.6 + - + +
30B MET* 3.6 36.3 - - + +
31B PHE* 3.6 40.8 - - + -
33B TRP* 3.7 22.4 - - + +
56B PHE* 3.8 22.2 - - + -
60B TYR* 3.8 17.5 - - + -
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Residues in contact with HIS 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LEU* 2.8 23.4 + - + +
4B LYS* 3.6 20.4 - - + +
6B ILE* 1.3 77.1 - - - +
8B LYS* 1.3 64.2 + - + +
10B LEU* 3.4 6.6 + - - +
11B ASN* 3.2 47.3 + - - -
30B MET* 4.2 6.9 - - + +
1148B K 2.5 33.3 - - - -
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Residues in contact with LYS 8 (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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374A MET 5.5 0.4 - - - -
375A GLY 5.5 1.3 - - - +
376A SER* 3.5 33.0 - - - +
380A LEU* 4.2 7.2 - - + -
382A LYS* 4.0 28.4 + - + +
385A ALA* 3.8 23.8 - - + -
4B LYS 3.1 17.1 + - - +
5B ARG* 3.2 8.2 + - - +
7B HIS* 1.3 78.3 - - + +
9B GLU* 1.3 54.7 + - - +
11B ASN* 3.2 9.7 + - + +
12B ASP* 2.8 60.3 + - - +
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Residues in contact with GLU 9 (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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5B ARG* 2.8 54.0 + - - +
6B ILE* 3.4 11.2 - - - +
8B LYS* 1.3 77.4 - - - +
10B LEU* 1.3 62.1 + - - +
12B ASP* 3.3 11.4 + - - +
13B LEU* 3.0 28.4 + - - +
33B TRP* 4.0 13.0 - - + -
56B PHE* 5.4 0.7 - - + -
60B TYR* 3.5 19.3 - - - +
98B THR* 3.5 17.3 - - - +
99B ILE* 2.8 37.9 + - + +
100B SER 4.5 0.7 + - - -
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Residues in contact with LEU 10 (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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6B ILE 3.1 12.8 + - - +
7B HIS* 3.7 10.3 - - - +
8B LYS 3.3 0.4 - - - -
9B GLU* 1.3 75.1 - - - +
11B ASN* 1.3 65.9 + - - +
13B LEU* 3.3 6.1 + - + +
14B ALA* 3.2 20.5 + - + +
23B ALA 4.4 6.1 - - - +
24B GLY* 4.2 7.4 - - - -
25B PRO* 3.7 37.2 - - + -
33B TRP* 3.7 15.6 - - + -
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Residues in contact with ASN 11 (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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374A MET 6.1 0.7 - - - +
375A GLY* 5.5 8.9 + - - +
7B HIS* 3.2 46.0 + - - +
8B LYS* 3.2 11.3 + - + +
10B LEU* 1.3 77.6 - - - +
12B ASP* 1.3 59.7 + - - +
14B ALA* 3.1 9.7 + - - +
15B ARG* 2.9 35.4 + - + +
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Residues in contact with ASP 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A MET* 4.1 12.8 - - - +
8B LYS* 2.8 59.7 + - - +
9B GLU* 3.3 14.5 + - - +
11B ASN* 1.3 75.2 - - - +
13B LEU* 1.3 58.4 + - + +
15B ARG* 4.4 4.7 - - - -
16B ASP* 2.9 35.6 + - - +
98B THR* 4.7 16.0 - - + +
100B SER* 6.4 2.7 - - - -
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLU* 3.0 17.2 + - - +
10B LEU* 3.7 9.0 - - + +
11B ASN 3.2 0.2 - - - -
12B ASP* 1.3 77.0 - - + +
14B ALA* 1.3 61.6 + - - +
16B ASP 4.3 2.0 - - - +
17B PRO* 3.3 26.5 - - - +
18B PRO* 3.6 34.4 - - + +
23B ALA* 3.8 24.7 - - + +
33B TRP* 3.5 33.7 - - + -
99B ILE* 4.3 15.7 - - + -
100B SER* 4.3 19.3 - - - +
103B LEU* 5.1 2.2 - - + -
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Residues in contact with ALA 14 (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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10B LEU 3.2 11.8 + - - +
11B ASN* 3.1 12.2 + - - +
13B LEU* 1.3 77.0 - - - +
15B ARG* 1.3 65.8 + - + +
17B PRO* 3.9 9.9 - - - +
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Residues in contact with ARG 15 (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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372A CYS 4.0 7.6 + - - -
373A GLU* 3.4 27.5 + - - +
374A MET 3.8 19.1 - - - +
375A GLY* 3.8 18.1 - - - -
11B ASN* 2.9 22.4 + - + +
12B ASP* 3.9 4.9 - - - +
14B ALA* 1.3 77.7 - - + +
16B ASP* 1.3 78.0 + - - +
17B PRO* 3.6 5.4 - - - +
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Residues in contact with ASP 16 (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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373A GLU 5.4 2.1 - - - +
374A MET* 4.3 22.5 - - - +
12B ASP* 2.9 17.7 + - - +
13B LEU* 3.7 3.7 - - - +
15B ARG* 1.3 95.1 - - - +
17B PRO* 1.3 67.7 - - - +
18B PRO* 3.3 8.0 - - - +
100B SER* 4.5 5.0 + - - -
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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