Contacts of the strand formed by residues 177 - 182 (chain A) in PDB entry 3SRG
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 HIS 177 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU* 4.8 0.2 - - - +
172A ALA* 3.4 1.0 - - - +
173A VAL* 2.7 48.0 + - + -
174A GLY* 3.2 18.7 + - - +
175A PRO* 3.9 12.3 - - + -
176A GLU* 1.3 98.0 + - + +
178A PHE* 1.3 60.1 + - - +
207A TYR* 4.3 8.1 - - - +
208A TYR 3.1 9.2 - - - +
209A SER* 3.7 10.3 - - - -
210A PRO* 3.4 31.3 - - + +
254A TRP* 6.1 2.5 - + + -
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Residues in contact with PHE 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU* 3.7 16.8 - - + -
141A VAL* 3.8 30.7 - - + -
159A ILE* 3.9 20.0 - - + -
164A LEU* 4.0 10.8 - - + -
170A ILE* 3.8 23.1 - - + -
171A VAL 3.1 20.4 - - - +
172A ALA* 3.9 3.1 - - - -
173A VAL* 4.1 4.3 - - - +
177A HIS* 1.3 82.2 - - - +
179A TYR* 1.3 61.6 + - - +
180A ALA* 3.8 22.4 - - + -
206A THR 3.9 0.2 - - - +
207A TYR* 3.7 3.0 - - - -
208A TYR* 2.8 71.0 + + + +
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Residues in contact with TYR 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ILE* 3.1 4.5 - - - +
171A VAL* 2.8 43.5 + - + +
173A VAL* 4.1 17.0 - - + -
178A PHE* 1.3 76.4 - - - +
180A ALA* 1.3 60.2 + - - +
205A VAL* 4.5 1.1 - - + -
206A THR 3.2 5.4 - - - +
207A TYR* 3.7 27.8 - + + -
216A VAL* 3.9 20.9 - - + -
226A ILE* 3.6 22.5 - - + +
235A VAL* 4.6 7.4 - - + -
250A LYS* 3.5 37.4 - - + +
254A TRP* 2.7 43.7 + + - +
256A LEU* 3.9 20.8 - - + +
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 3.5 31.2 - - + -
167A VAL* 4.1 7.2 - - + -
169A ASP 3.4 6.1 - - - +
170A ILE* 3.7 18.6 - - + -
178A PHE* 3.8 6.7 - - + -
179A TYR* 1.3 75.4 - - - +
181A THR* 1.3 62.9 + - - +
182A ASN* 4.0 0.3 + - - -
205A VAL* 3.2 6.8 - - - +
206A THR* 2.9 33.2 + - - +
226A ILE* 4.6 0.7 - - - -
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Residues in contact with THR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A VAL* 3.3 7.3 - - - +
168A ASN* 2.9 27.5 + - - +
169A ASP 3.0 17.7 + - - -
180A ALA* 1.3 74.4 - - - +
182A ASN* 1.3 60.5 + - - +
183A ASP 4.0 0.2 - - - -
204A PHE 3.9 3.8 - - - -
205A VAL* 4.0 13.0 - - + -
223A ALA* 3.9 27.4 - - + -
224A ASN 2.6 29.3 + - - +
225A GLY 3.9 5.6 - - - +
226A ILE* 3.7 23.3 - - + +
237A ILE* 4.1 2.7 - - + -
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Residues in contact with ASN 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU 3.2 20.8 + - - -
164A LEU* 3.3 8.5 - - - +
165A PRO* 3.1 15.9 - - - +
166A SER 3.1 27.6 + - - +
167A VAL* 3.6 6.9 - - - +
180A ALA 4.4 1.0 + - - -
181A THR* 1.3 74.9 - - - +
183A ASP* 1.3 59.3 + - - +
184A HIS 3.1 20.3 + - - +
203A SER* 2.7 22.5 + - - -
204A PHE* 2.8 41.7 + - + +
206A THR* 3.4 8.5 + - - -
223A ALA* 4.0 2.1 - - - +
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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