Contacts of the strand formed by residues 203 - 208 (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 SER 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A ASN 2.7 22.4 + - - -
183A ASP 3.5 19.1 - - - -
184A HIS* 4.4 7.2 - - - -
195A GLU* 4.4 1.6 + - - -
202A TRP* 1.3 78.2 - - - +
204A PHE* 1.3 59.3 + - - +
219A GLY 3.0 10.6 + - - -
220A PHE* 3.0 37.6 + - - +
222A PHE 3.8 5.2 - - - -
223A ALA* 2.9 24.8 + - - +
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Residues in contact with PHE 204 (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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162A LYS 5.0 1.1 - - - -
163A LEU* 3.5 13.5 - - + -
165A PRO* 3.7 28.9 - - + -
181A THR 3.8 0.2 - - - -
182A ASN* 2.8 49.2 + - + +
185A TYR* 4.2 24.2 - + - -
202A TRP 3.5 15.3 - - - +
203A SER* 1.3 78.4 + - - +
205A VAL* 1.3 65.6 + - - +
206A THR* 3.2 26.7 - - - -
215A VAL* 3.8 26.7 - - + -
217A ALA 3.4 12.8 - - - +
218A GLU* 3.8 14.1 - - + +
220A PHE* 4.1 3.6 - - - -
223A ALA* 4.8 0.4 - - - +
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Residues in contact with VAL 205 (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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179A TYR* 4.5 2.9 - - + -
180A ALA 3.2 11.9 - - - +
181A THR* 4.0 18.6 - - + -
204A PHE* 1.3 79.9 - - - +
206A THR* 1.3 61.8 + - - +
215A VAL* 3.5 4.5 - - - +
216A VAL* 2.7 50.0 + - + -
217A ALA* 2.8 16.1 + - + +
220A PHE* 3.9 16.2 - - + -
223A ALA* 4.4 1.6 - - + -
226A ILE* 3.8 20.6 - - + -
237A ILE* 3.8 28.5 - - + -
256A LEU* 4.9 0.2 - - + -
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Residues in contact with THR 206 (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* 2.6 34.0 + - + +
164A LEU* 3.9 19.3 - - + -
178A PHE 3.9 0.3 - - - +
179A TYR* 3.2 4.7 - - - +
180A ALA* 2.9 32.5 + - - +
182A ASN* 3.4 1.3 + - - -
204A PHE* 3.2 18.9 - - - -
205A VAL* 1.3 70.7 - - - +
207A TYR* 1.3 73.4 + - - +
208A TYR* 4.0 2.2 + - + +
213A VAL* 3.7 20.6 - - + -
214A ARG 3.4 7.9 - - - +
215A VAL* 4.5 1.6 - - - +
216A VAL* 4.4 2.7 - - - -
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Residues in contact with TYR 207 (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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173A VAL* 4.1 13.0 - - + -
177A HIS* 4.3 9.8 - - + +
178A PHE 3.7 7.2 - - - -
179A TYR* 3.7 25.8 - + + -
206A THR* 1.3 75.7 - - - +
208A TYR* 1.3 65.5 + - - +
209A SER* 3.5 35.3 - - - -
212A ASP* 3.9 18.6 - - + -
213A VAL* 3.3 4.9 - - - -
214A ARG* 2.8 43.9 + - + +
216A VAL* 3.8 25.5 - - + +
254A TRP* 3.6 59.9 + + + +
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Residues in contact with TYR 208 (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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157A LYS* 4.9 9.2 + - - -
159A ILE* 3.4 40.2 - - + +
160A ARG 4.6 2.4 + - - -
161A HIS* 4.2 13.7 - + + -
164A LEU* 4.0 13.7 - - + -
176A GLU* 3.6 19.6 + - + -
177A HIS* 3.1 4.9 - - - -
178A PHE* 2.8 72.1 + + + +
206A THR* 3.9 2.9 - - + -
207A TYR* 1.3 78.6 - - - +
209A SER* 1.3 76.0 + - - +
210A PRO* 4.4 5.6 - - + +
212A ASP 4.2 0.7 - - - -
213A VAL* 3.6 29.4 - - + -
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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