Contacts of the strand formed by residues 178 - 185 (chain B) in PDB entry 4Y2H
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 LEU 178 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B GLN* 4.7 5.6 + - - +
149B VAL* 3.6 17.4 - - + +
150B ASP 3.8 4.9 - - - +
151B ALA* 3.7 33.0 - - - +
152B ILE* 3.9 15.9 - - + +
173B ALA 3.6 2.0 + - - -
174B ARG* 3.0 47.2 + - + +
175B THR 5.2 2.1 - - - +
176B LYS 5.5 0.2 - - - -
177B TRP* 1.3 76.8 + - - +
179B LYS* 1.3 70.7 + - - +
180B GLU* 3.7 0.9 + - - -
182B GLY* 3.7 24.0 - - - +
183B LEU 3.7 9.6 - - - +
184B LEU* 4.9 4.0 - - + -
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Residues in contact with LYS 179 (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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85B THR* 4.8 1.0 + - - +
147B GLU* 5.5 3.6 + - - -
148B GLN* 3.8 43.2 + - + +
149B VAL 2.9 18.8 + - - +
150B ASP* 2.7 41.0 + - - +
177B TRP 3.5 1.6 + - - -
178B LEU* 1.3 79.5 - - - +
180B GLU* 1.3 63.8 + - - +
181B GLY 3.2 0.3 + - - -
182B GLY* 2.9 25.2 + - - +
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Residues in contact with GLU 180 (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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148B GLN* 5.1 0.6 + - - -
178B LEU 3.7 1.8 + - - -
179B LYS* 1.3 75.6 - - - +
181B GLY* 1.3 63.3 + - - +
182B GLY 3.4 0.2 + - - -
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Residues in contact with GLY 181 (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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179B LYS 3.2 0.8 + - - -
180B GLU* 1.3 78.4 - - - +
182B GLY* 1.3 65.7 + - - +
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Residues in contact with GLY 182 (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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150B ASP* 3.4 14.6 - - - -
178B LEU* 3.7 18.3 - - - +
179B LYS* 2.9 20.0 + - - -
180B GLU 3.2 1.0 + - - -
181B GLY* 1.3 82.2 - - - +
183B LEU* 1.3 62.2 + - - +
184B LEU* 4.0 1.4 + - - +
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Residues in contact with LEU 183 (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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77B ASN* 4.0 31.2 - - + +
80B ALA* 4.2 18.6 - - + -
81B LEU* 4.4 13.7 - - + -
150B ASP 2.9 9.3 + - - +
151B ALA* 3.1 13.0 - - + -
152B ILE 2.8 30.7 + - - -
178B LEU* 3.7 5.0 - - - +
182B GLY* 1.3 74.1 - - - -
184B LEU* 1.3 60.9 + - - +
185B LEU* 4.2 13.9 - - + -
297B PRO* 3.8 27.1 - - + -
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Residues in contact with LEU 184 (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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152B ILE* 3.6 30.3 - - + +
154B SER* 6.4 0.4 - - - -
170B VAL* 4.5 15.5 - - + -
171B LEU* 5.8 0.7 - - + -
174B ARG* 3.9 32.5 - - + +
178B LEU* 4.9 4.0 - - + -
182B GLY 4.0 1.7 + - - +
183B LEU* 1.3 78.2 - - - +
185B LEU* 1.3 77.4 + - - +
186B PRO 3.3 20.5 - - - +
187B ALA* 3.4 17.2 + - + +
258B LEU* 3.5 35.7 - - + -
259B SER* 4.6 3.8 - - - +
297B PRO* 3.7 2.8 - - - +
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Residues in contact with LEU 185 (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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73B GLY 4.3 2.7 - - - +
74B ILE* 4.2 32.5 - - + +
77B ASN* 4.0 18.2 - - + +
81B LEU* 4.9 10.3 - - + -
100B CYS* 6.1 0.7 - - - -
151B ALA* 5.8 2.0 - - + -
152B ILE 2.9 15.3 + - - +
153B VAL* 3.4 16.7 - - + +
154B SER* 3.1 26.0 + - - +
183B LEU* 4.2 19.5 - - + -
184B LEU* 1.3 85.1 - - - +
186B PRO* 1.3 64.5 + - - +
296B PHE* 3.9 16.8 - - + -
297B PRO* 3.5 27.6 - - + -
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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