Contacts of the helix formed by residues 15 - 28 (chain B) in PDB entry 5C58
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 SER 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLY 4.0 0.4 + - - -
14B TYR* 1.3 74.9 - - - +
16B ILE* 1.3 64.1 + - - +
17B HIS* 3.9 2.9 + - - +
18B ASP* 2.7 41.0 + - - +
19B TYR* 3.2 16.5 + - - +
162B VAL 4.2 0.8 + - - -
163B ASN* 3.9 14.0 - - - -
164B SER 3.3 21.5 - - - -
165B THR* 3.8 6.7 - - - +
166B PHE* 3.2 14.1 - - - -
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Residues in contact with ILE 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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3B PHE* 6.6 0.2 - - + -
5B VAL* 6.4 0.9 - - + -
15B SER* 1.3 72.7 - - - +
17B HIS* 1.3 63.8 + - - +
19B TYR* 3.4 4.0 + - - +
20B LEU* 3.4 29.5 + - + +
115B PHE* 4.3 23.8 - - + -
151B LEU* 4.2 22.9 - - + -
155B LEU* 4.5 10.8 - - + -
161B SER 4.0 12.6 - - - +
162B VAL* 3.2 18.8 - - + +
164B SER 3.0 15.9 + - - +
165B THR 4.9 0.2 - - - +
166B PHE* 3.9 26.4 - - + -
169B VAL* 4.0 29.6 - - + -
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Residues in contact with HIS 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B SER* 3.4 3.3 - - - +
16B ILE* 1.3 74.0 - - - +
18B ASP* 1.3 76.4 + - - +
19B TYR 3.2 1.2 + - - -
20B LEU* 3.4 3.2 + - - +
21B GLY* 3.3 21.1 + - - -
148B GLU* 3.3 34.9 + - - -
162B VAL* 2.7 30.4 + - + +
163B ASN* 3.8 19.3 - - - +
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Residues in contact with ASP 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR* 4.8 12.6 - - + -
15B SER* 2.7 31.3 + - - +
17B HIS* 1.3 90.0 - - - +
19B TYR* 1.3 59.4 + - - +
21B GLY* 4.3 1.5 - - - -
22B GLN* 3.4 25.9 + - - +
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Residues in contact with TYR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 4.5 19.5 - + - -
14B TYR* 5.1 7.4 - + + +
15B SER 3.2 17.2 + - - +
16B ILE 3.6 4.0 - - - +
17B HIS 3.1 1.2 - - - -
18B ASP* 1.3 77.6 - - - +
20B LEU* 1.3 74.0 + - + +
22B GLN* 2.9 10.3 + - + +
23B TRP* 2.7 56.9 + + + +
94B PHE* 3.6 25.1 - + + +
95B GLY 4.2 0.5 + - - -
112B ASP* 3.2 38.8 + - + +
113B VAL* 3.6 32.3 - - + -
115B PHE* 6.1 0.2 - + - -
166B PHE* 3.9 11.4 - + + -
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 3.4 26.6 + - + +
17B HIS 3.4 3.6 + - - +
19B TYR* 1.3 94.4 - - + +
21B GLY* 1.3 57.5 + - - +
23B TRP* 3.3 6.2 + - + +
24B ALA* 3.0 27.5 + - - +
94B PHE* 4.6 16.2 - - + -
115B PHE* 4.7 8.3 - - + -
144B THR* 3.5 28.0 - - + +
147B LEU* 3.9 32.3 - - + -
148B GLU* 3.7 30.7 - - + +
151B LEU* 5.0 2.0 - - + -
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Residues in contact with GLY 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B HIS* 3.3 13.8 + - - -
18B ASP* 4.6 0.9 - - - -
19B TYR 3.2 0.8 - - - -
20B LEU* 1.3 77.8 - - - +
22B GLN* 1.3 60.9 + - - +
24B ALA* 3.4 7.0 + - - +
25B SER* 3.3 20.4 + - - -
144B THR* 4.6 2.6 + - - -
148B GLU* 5.2 1.2 + - - -
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Residues in contact with GLN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A ARG* 4.7 17.4 - - - +
14B TYR* 3.7 33.4 + - - -
18B ASP 3.4 19.6 + - - +
19B TYR* 2.9 9.8 + - + +
21B GLY* 1.3 74.3 - - - +
23B TRP* 1.3 63.1 + - - +
24B ALA 3.3 0.2 - - - -
25B SER* 2.8 25.4 + - - +
26B THR* 3.6 13.8 + - + +
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Residues in contact with TRP 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 2.7 51.3 + + + +
20B LEU* 3.5 9.6 - - + +
21B GLY 3.2 0.2 - - - -
22B GLN* 1.3 74.5 - - - +
24B ALA* 1.3 64.4 + - + +
26B THR* 3.0 8.0 + - - -
27B PHE* 3.0 63.2 + + + +
65B THR* 3.7 18.5 - - + +
66B ALA 3.8 18.3 + - - -
67B PHE* 3.7 22.4 - + - -
94B PHE* 3.6 30.0 - + + +
95B GLY* 4.2 5.3 - - - +
96B ASP* 5.7 0.9 - - - -
112B ASP* 5.7 0.7 - - - -
139B LEU* 4.1 24.7 - - + -
142B GLY* 5.3 1.3 - - - -
144B THR* 4.2 15.7 - - + -
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU 3.0 15.4 + - - +
21B GLY* 3.4 7.6 + - - +
22B GLN 3.3 0.2 - - - -
23B TRP* 1.3 84.5 - - + +
25B SER* 1.3 60.6 - - - +
26B THR 3.2 0.7 - - - -
27B PHE* 3.7 5.2 - - - -
28B GLY* 2.9 26.3 + - - +
142B GLY* 3.4 31.2 - - - +
144B THR* 4.5 3.6 - - + -
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Residues in contact with SER 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLY 3.3 12.3 + - - -
22B GLN* 2.8 30.3 + - - +
24B ALA* 1.3 78.0 - - - +
26B THR* 1.3 63.7 + - - +
28B GLY* 4.7 1.8 + - - -
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Residues in contact with THR 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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542A ARG* 4.5 19.1 - - - +
544A THR* 4.6 20.1 - - + +
22B GLN* 3.6 15.8 + - + +
23B TRP* 3.0 17.0 + - - -
25B SER* 1.3 84.7 + - - +
27B PHE* 1.3 61.4 + - - +
61B ALA* 4.8 3.5 - - - +
62B ASN* 2.9 25.6 + - - -
65B THR* 4.4 8.8 + - - +
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Residues in contact with PHE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TRP* 3.0 45.7 + + + +
24B ALA* 4.0 4.7 - - - -
26B THR* 1.3 80.5 + - - +
28B GLY* 1.3 77.8 + - - +
30B VAL* 3.4 30.7 - - + -
57B ILE* 4.1 10.5 - - + -
58B SER 4.3 0.7 - - - -
59B SER* 2.5 40.2 + - - -
61B ALA* 3.7 7.2 - - - +
65B THR* 3.1 39.5 - - + -
66B ALA* 4.0 9.0 - - - -
67B PHE* 4.4 6.1 - + - -
139B LEU 3.2 26.7 - - - -
140B MET* 4.8 0.2 - - - -
142B GLY* 4.7 1.8 - - - -
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Residues in contact with GLY 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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24B ALA 2.9 21.1 + - - -
25B SER 5.4 1.8 - - - -
26B THR 3.8 0.6 - - - -
27B PHE* 1.3 90.1 - - - +
29B ASP* 1.3 61.9 + - - -
30B VAL* 5.4 0.2 - - - -
61B ALA* 5.2 4.0 - - - -
142B GLY* 3.3 18.8 + - - -
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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
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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