Contacts of the strand formed by residues 152 - 160 (chain I) in PDB entry 2A3W
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 152 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10I VAL* 3.6 2.3 - - - -
11I PHE* 2.8 37.2 + - - +
40I TYR 3.4 11.2 - - - -
150I PHE* 3.4 10.8 - - - -
151I VAL* 1.3 75.5 - - - +
153I GLU* 1.3 63.9 + - - -
115J VAL* 3.6 16.8 - - - -
116J LYS 4.7 1.6 - - - -
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Residues in contact with GLU 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I VAL* 3.4 20.2 - - + +
9I PHE 3.2 6.5 - - - +
10I VAL* 4.0 13.7 - - + -
39I ALA* 3.2 5.5 - - - -
40I TYR* 2.9 35.2 + - - +
150I PHE* 3.6 2.2 - - - -
152I GLY* 1.3 80.4 - - - +
154I ILE* 1.3 65.7 + - - +
200I PRO 4.9 0.5 - - - +
202I VAL* 5.9 0.2 - - - +
203I TRP* 2.7 46.6 + - + +
114J LEU 4.2 1.9 - - - +
115J VAL* 4.0 5.0 - - - -
116J LYS* 3.1 49.1 + - + +
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Residues in contact with ILE 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I VAL* 3.3 4.5 - - - -
9I PHE* 2.8 37.5 + - + -
11I PHE* 4.2 12.8 - - + -
37I PHE* 4.6 15.5 - - + -
38I ARG 3.3 7.2 - - - +
39I ALA* 4.3 8.3 - - + -
49I LEU* 4.0 18.8 - - + +
133I LEU* 4.0 35.7 - - + -
134I GLY 5.1 0.7 - - - +
150I PHE* 3.4 40.6 - - + -
153I GLU* 1.3 75.3 - - - +
155I GLY* 1.3 68.0 + - - +
157I LEU* 4.7 7.9 - - + -
185I TRP* 3.7 6.5 - - + -
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Residues in contact with GLY 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I LYS 4.1 0.9 - - - -
8I VAL* 3.9 15.2 - - - +
37I PHE* 3.7 4.3 - - - +
38I ARG* 2.9 31.3 + - - +
154I ILE* 1.3 75.2 - - - +
156I ASP* 1.3 72.6 + - - -
157I LEU* 3.2 4.1 + - - -
185I TRP* 3.5 14.8 - - - -
201I LEU* 6.0 0.9 - - - -
203I TRP* 5.0 0.6 - - - -
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Residues in contact with ASP 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I SER* 5.8 0.2 - - - -
6I GLY 5.1 6.2 + - - -
7I LYS 5.1 1.2 + - - +
36I CYS* 3.4 2.4 - - - +
37I PHE* 3.3 14.8 + - - -
38I ARG* 2.6 43.3 + - + +
93I HIS* 5.2 4.3 + - + +
155I GLY* 1.3 71.5 - - - +
157I LEU* 1.3 59.7 + - - +
158I TYR* 3.2 27.8 + - + -
172I ALA 5.9 0.9 - - - +
175I GLY* 5.9 0.6 - - - -
185I TRP* 3.4 27.8 + - - +
186I GLN* 5.8 0.2 + - - -
201I LEU* 4.0 18.2 - - - +
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Residues in contact with LEU 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I LEU* 4.3 9.0 - - + -
35I LEU* 3.8 20.0 - - + -
36I CYS 3.3 5.6 - - - -
37I PHE* 3.9 23.6 - - + -
49I LEU 5.8 0.2 - - - +
50I PHE* 4.1 22.0 - - + -
133I LEU* 4.2 18.4 - - + -
154I ILE* 4.7 5.4 - - + -
155I GLY 3.3 1.3 - - - +
156I ASP* 1.3 74.7 - - - +
158I TYR* 1.3 62.5 + - - +
183I LEU* 3.9 30.5 - - + -
184I ASP* 3.9 2.1 - - - -
185I TRP* 3.1 51.9 + - + +
188I LEU* 4.8 2.1 - - + +
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Residues in contact with TYR 158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I LEU* 3.4 5.0 - - - +
36I CYS* 2.8 36.3 + - + +
156I ASP* 3.2 36.6 + - + -
157I LEU* 1.3 75.6 - - - +
159I MET* 1.3 60.5 + - - +
160I TRP* 3.4 27.9 - + + -
172I ALA* 5.8 1.3 - - + -
177I PRO* 3.5 32.8 - - + +
178I LEU 4.6 5.4 - - - -
179I PRO* 6.0 0.2 - - + -
180I ALA* 4.1 4.9 - - + -
183I LEU 3.4 5.2 - - - +
184I ASP* 3.6 35.7 - - - -
185I TRP* 3.6 18.8 - - + +
186I GLN* 2.9 34.2 + - - -
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Residues in contact with MET 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I LEU* 3.8 23.6 - - + -
33I PHE* 3.9 15.3 - - + -
34I THR 3.2 13.7 - - - +
35I LEU* 4.0 13.7 - - + -
50I PHE* 4.0 23.3 - - + -
52I TYR* 4.8 7.4 - - + -
61I LEU* 3.7 29.8 - - + -
131I ILE* 5.3 0.9 - - - -
158I TYR* 1.3 74.3 - - - +
160I TRP* 1.3 63.4 + - - +
180I ALA* 3.3 7.0 - - - +
182I ILE* 3.0 44.3 + - + -
183I LEU* 2.9 31.0 + - + +
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Residues in contact with TRP 160 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I PHE* 3.2 9.7 - - - +
34I THR* 2.8 51.2 + - - +
36I CYS* 3.6 32.1 - - + -
158I TYR* 3.4 32.1 - + + -
159I MET* 1.3 75.8 - - - +
161I ASP* 1.3 58.5 + - - +
162I SER* 3.2 11.7 - - - +
164I LEU* 3.5 46.6 - - + +
168I ASN 5.8 0.2 - - - -
172I ALA* 4.4 9.6 - - + -
177I PRO* 4.3 3.1 - - + -
178I LEU* 3.2 44.3 + - + +
179I PRO 3.2 17.0 + - - -
180I ALA* 3.5 12.4 - - + +
181I ASN* 3.5 7.9 - - - +
182I ILE* 3.5 6.6 - - - +
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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