Contacts of the strand formed by residues 152 - 160 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10K VAL* 3.4 2.9 - - - -
11K PHE* 2.6 48.8 + - - +
40K TYR 3.4 9.6 - - - -
150K PHE* 3.4 7.0 - - - -
151K VAL* 1.3 75.3 - - - +
153K GLU* 1.3 62.3 + - - -
115L VAL* 3.6 16.6 - - - -
116L LYS 4.6 2.7 - - - -
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Residues in contact with GLU 153 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K VAL* 3.3 17.5 - - + +
9K PHE 3.2 6.1 - - - +
10K VAL* 3.9 16.6 - - + -
39K ALA* 3.2 4.3 - - - -
40K TYR* 2.9 37.6 + - + +
150K PHE* 3.4 2.6 - - - -
152K GLY* 1.3 80.7 - - - +
154K ILE* 1.3 67.0 + - - +
200K PRO 4.9 0.2 - - - +
203K TRP* 2.7 46.9 + - + +
114L LEU 4.3 1.7 - - - +
115L VAL* 4.0 4.9 - - - -
116L LYS* 3.0 49.4 + - + +
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Residues in contact with ILE 154 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K VAL* 3.4 5.0 - - - -
9K PHE* 2.8 36.5 + - + +
11K PHE* 4.1 16.6 - - + -
37K PHE* 4.6 7.9 - - + -
38K ARG 3.2 10.8 - - - +
39K ALA* 4.2 6.5 - - + -
49K LEU* 4.1 22.7 - - + +
133K LEU* 4.2 26.0 - - + -
134K GLY 5.2 0.7 - - - +
150K PHE* 3.5 36.3 - - + -
153K GLU* 1.3 79.8 - - - +
155K GLY* 1.3 67.1 + - - +
157K LEU* 4.6 15.9 - - + -
185K TRP* 3.7 6.9 - - + -
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Residues in contact with GLY 155 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K LYS 4.1 0.9 - - - -
8K VAL* 3.9 15.2 - - - +
37K PHE* 3.7 3.1 - - - +
38K ARG* 2.8 38.1 + - - +
154K ILE* 1.3 75.7 - - - +
156K ASP* 1.3 65.4 + - - -
157K LEU* 3.2 4.0 + - - -
185K TRP* 3.6 13.9 - - - -
201K LEU* 6.0 0.7 - - - -
203K TRP* 4.8 0.4 - - - -
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Residues in contact with ASP 156 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K SER* 5.6 0.2 - - - -
6K GLY 5.0 6.6 + - - -
7K LYS 5.1 1.2 - - - +
36K CYS* 3.4 2.8 - - - +
37K PHE* 3.3 14.3 - - - -
38K ARG* 2.8 42.2 + - + +
93K HIS* 5.0 4.4 + - + +
155K GLY* 1.3 72.6 - - - +
157K LEU* 1.3 59.9 + - - +
158K TYR* 3.2 28.3 + - + -
172K ALA 5.8 1.3 - - - +
175K GLY* 5.6 1.6 - - - -
185K TRP* 3.4 28.6 + - - +
201K LEU* 4.5 14.2 - - - +
204K VAL* 5.8 0.2 - - - +
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Residues in contact with LEU 157 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K LEU* 4.4 9.9 - - + -
35K LEU* 3.7 17.5 - - + -
36K CYS 3.3 5.2 - - - -
37K PHE* 3.7 28.0 - - + -
49K LEU 5.7 0.7 - - - +
50K PHE* 4.0 22.0 - - + -
133K LEU* 4.3 15.9 - - + -
154K ILE* 4.6 6.1 - - + -
155K GLY 3.2 1.3 + - - +
156K ASP* 1.3 74.6 - - - +
158K TYR* 1.3 63.1 + - - +
183K LEU* 4.0 30.1 - - + -
184K ASP* 3.9 2.3 - - - -
185K TRP* 3.1 51.4 + - + +
188K LEU* 4.5 1.9 - - + +
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Residues in contact with TYR 158 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K SER* 5.2 0.7 + - - -
35K LEU* 3.4 4.0 - - - +
36K CYS* 2.8 39.6 + - + +
156K ASP* 3.2 44.0 + - + -
157K LEU* 1.3 74.8 - - - +
159K MET* 1.3 60.9 + - - +
160K TRP* 3.4 26.8 - + + -
172K ALA* 5.8 1.8 - - + -
177K PRO* 3.6 32.1 - - + +
178K LEU 4.8 3.4 - - - -
179K PRO* 6.2 0.2 - - + -
180K ALA* 4.1 4.9 - - + -
183K LEU 3.3 5.8 - - - +
184K ASP* 3.4 34.3 - - - -
185K TRP* 3.5 27.2 - - + +
186K GLN* 2.9 29.0 + - - +
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Residues in contact with MET 159 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K LEU* 3.8 26.9 - - + -
33K PHE* 3.8 26.7 - - + -
34K THR 3.2 13.7 - - - +
35K LEU* 4.0 13.2 - - + -
50K PHE* 4.0 24.2 - - + -
52K TYR* 4.8 7.2 - - + -
61K LEU* 3.8 15.0 - - + -
131K ILE* 5.5 0.7 - - - -
158K TYR* 1.3 74.1 - - - +
160K TRP* 1.3 65.7 + - - +
180K ALA* 3.3 7.0 - - - +
182K ILE* 3.1 42.3 + - + -
183K LEU* 2.8 31.9 + - + +
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Residues in contact with TRP 160 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K PHE* 3.3 6.1 - - - +
34K THR* 2.8 39.0 + - - +
36K CYS* 3.7 23.3 - - + -
158K TYR* 3.4 36.8 - + + -
159K MET* 1.3 76.9 - - - +
161K ASP* 1.3 59.8 + - - +
162K SER* 3.2 15.5 - - - +
164K LEU* 3.6 47.5 - - + +
168K ASN 5.7 0.2 - - - -
172K ALA* 4.6 9.4 - - + -
177K PRO* 4.4 3.1 - - + -
178K LEU* 3.2 33.9 + - + +
179K PRO 3.1 27.2 + - - -
180K ALA* 3.5 10.7 - - + +
181K ASN* 3.5 10.1 - - - +
182K ILE* 3.4 11.8 - - - +
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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