Contacts of the helix formed by residues 13 - 27 (chain B) in PDB entry 2W5U
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 GLY 13 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B THR* 2.8 19.5 + - - +
11B ASP 3.6 1.4 - - - -
12B SER* 1.3 77.8 - - - +
14B ASN* 1.3 64.0 + - - +
15B ALA 3.4 2.2 - - - -
16B GLU* 3.3 19.4 + - - +
17B ALA* 2.9 24.7 + - - +
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Residues in contact with ASN 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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12B SER* 3.3 7.3 + - - -
13B GLY* 1.3 75.0 - - - +
15B ALA* 1.3 57.4 + - - +
17B ALA* 3.1 9.1 + - - +
18B ILE* 2.9 31.0 + - - +
86B LEU* 3.7 8.7 - - + -
141B GLU* 3.6 32.6 + - + +
142B ASP* 4.8 4.0 - - - +
165B FMN 2.8 45.9 + - - +
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Residues in contact with ALA 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 4.0 10.0 - - + +
9B GLY 3.3 27.6 - - - +
14B ASN* 1.3 73.8 - - - +
16B GLU* 1.3 57.1 + - - +
18B ILE* 3.8 3.2 - - - +
19B ALA* 2.9 30.8 + - - +
51B VAL* 4.3 5.5 - - + +
53B PRO* 3.8 12.8 - - + -
86B LEU* 3.4 20.5 - - + +
165B FMN 2.8 15.8 + - - +
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Residues in contact with GLU 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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8B PHE* 4.0 38.3 - - + -
10B THR* 4.0 10.8 + - + +
13B GLY* 3.3 24.0 + - - +
14B ASN 3.2 0.4 - - - -
15B ALA* 1.3 77.9 - - - +
17B ALA* 1.3 61.7 + - - +
19B ALA* 3.3 2.9 + - - +
20B GLU* 3.1 26.9 + - + +
31B VAL* 5.4 0.7 - - + +
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Residues in contact with ALA 17 (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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13B GLY 2.9 13.4 + - - +
14B ASN* 3.4 11.2 - - - +
16B GLU* 1.3 76.3 - - - +
18B ILE* 1.3 58.7 + - + +
20B GLU* 3.2 8.1 + - - +
21B LYS* 2.9 43.3 + - - +
141B GLU* 6.2 0.7 - - + +
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Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ASN 2.9 18.3 + - - +
15B ALA* 3.8 5.4 - - - +
17B ALA* 1.3 75.9 - - + +
19B ALA* 1.3 58.0 + - - +
21B LYS* 3.2 17.6 + - + +
22B ILE* 2.9 47.2 + - + +
51B VAL* 4.1 6.1 - - + -
84B VAL* 4.0 19.3 - - + -
86B LEU* 3.9 18.4 - - + -
139B ILE* 4.0 11.0 - - + -
141B GLU* 4.5 7.0 - - + +
148B THR* 3.1 36.3 - - + -
152B ILE* 4.0 7.9 - - + -
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Residues in contact with ALA 19 (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* 3.8 18.7 - - + +
8B PHE* 3.7 19.7 - - + -
15B ALA 2.9 20.0 + - - +
16B GLU 3.3 5.1 + - - +
18B ILE* 1.3 77.0 - - - +
20B GLU* 1.3 58.0 + - - +
22B ILE* 3.4 4.6 + - - +
23B SER* 3.0 26.3 + - - -
31B VAL* 3.8 5.7 - - + +
51B VAL* 3.7 23.1 - - + -
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Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLU* 3.1 15.9 + - + +
17B ALA* 3.5 10.5 - - - +
19B ALA* 1.3 73.1 - - - +
21B LYS* 1.3 60.6 + - - +
23B SER* 3.1 18.1 + - - -
24B LYS* 2.9 57.5 + - - +
31B VAL* 4.3 14.7 - - + +
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Residues in contact with LYS 21 (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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17B ALA* 2.9 25.1 + - - +
18B ILE* 3.3 33.7 - - + +
20B GLU* 1.3 73.1 - - - +
22B ILE* 1.3 63.8 + - - +
24B LYS* 3.4 25.1 + - - +
25B ALA* 3.0 26.4 + - - +
141B GLU* 5.5 4.5 - - - -
148B THR* 4.5 8.9 - - + +
149B ASP* 2.6 36.5 + - - +
152B ILE* 3.9 14.5 - - + +
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 4.2 8.3 - - + -
18B ILE* 2.9 33.1 + - + +
19B ALA* 3.7 4.9 - - - +
21B LYS* 1.3 76.1 - - - +
23B SER* 1.3 59.1 + - - +
25B ALA* 3.1 1.5 + - - -
26B ILE* 2.8 37.2 + - + +
49B ILE* 4.1 28.7 - - + -
51B VAL* 4.0 9.2 - - + -
84B VAL* 3.7 31.0 - - + -
137B LEU* 4.3 4.7 - - + -
152B ILE* 3.3 28.0 - - + -
155B TRP* 4.4 5.4 - - + -
156B VAL* 4.4 11.7 - - + -
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Residues in contact with SER 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 3.7 13.2 - - - +
19B ALA 3.0 6.6 + - - -
20B GLU* 3.1 17.3 + - - -
22B ILE* 1.3 76.0 - - - +
24B LYS* 1.3 54.8 + - - +
27B GLY* 2.8 35.2 + - - -
29B ALA* 3.7 21.2 + - - +
31B VAL* 3.6 29.5 - - - +
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Residues in contact with LYS 24 (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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20B GLU* 2.9 47.1 + - - +
21B LYS* 3.7 26.5 - - - +
23B SER* 1.3 72.7 - - - +
25B ALA* 1.3 59.4 + - - +
27B GLY* 4.4 3.8 + - - -
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Residues in contact with ALA 25 (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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21B LYS 3.0 18.0 + - - +
22B ILE 3.1 3.1 + - - +
24B LYS* 1.3 78.1 - - - +
26B ILE* 1.3 59.3 + - - +
152B ILE* 4.0 11.2 - - + +
153B SER* 5.5 3.6 - - - -
156B VAL* 3.6 28.6 - - + +
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Residues in contact with ILE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.1 11.7 - - + +
6B ILE* 4.7 1.8 - - + -
22B ILE* 2.8 30.3 + - + +
23B SER 4.0 1.8 - - - +
25B ALA* 1.3 74.1 - - - +
27B GLY* 1.3 74.2 + - - +
28B ASN* 5.1 0.9 - - - +
29B ALA* 4.2 11.4 - - + -
49B ILE* 3.9 24.2 - - + -
155B TRP* 6.1 0.2 - - + -
156B VAL* 3.7 29.8 - - + +
159B VAL* 4.5 9.4 - - + -
160B ARG* 5.2 6.5 - - + +
163B PHE* 4.0 27.4 - - + +
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Residues in contact with GLY 27 (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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4B ILE* 4.6 3.5 - - - +
23B SER 2.8 17.9 + - - -
24B LYS 4.3 3.7 + - - -
25B ALA 3.6 1.6 - - - -
26B ILE* 1.3 87.5 - - - +
28B ASN* 1.3 71.3 - - - +
29B ALA* 2.9 11.2 + - - +
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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