Contacts of the strand formed by residues 203 - 210 (chain T) in PDB entry 2IAN
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 203 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156T TRP* 3.8 1.0 + - + +
157T VAL* 3.5 6.1 - - - +
158T ASN* 3.0 40.3 + - - +
159T GLY* 4.7 12.3 + - - -
201T ARG 3.6 0.6 + - - -
202T ASN* 1.3 73.6 - - - +
204T PHE* 1.3 62.8 + - - +
205T ARG* 3.7 38.2 - - + +
234T GLU* 2.7 35.7 + - + +
235T ALA 4.0 2.0 - - - -
236T TRP* 3.5 46.9 - + + -
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Residues in contact with PHE 204 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123T VAL* 5.3 1.4 - - + +
139T LEU* 3.7 26.5 - - + -
155T TRP* 5.1 3.1 - - + -
156T TRP 3.5 2.7 - - - +
157T VAL* 3.7 21.3 - - + -
190T LEU* 3.7 17.7 - - + -
192T VAL* 4.4 9.9 - - + -
196T PHE* 3.7 39.3 - + - -
197T TRP* 3.4 38.6 - + - -
202T ASN* 3.6 24.9 - - + -
203T HIS* 1.3 73.8 - - - +
205T ARG* 1.3 61.6 + - - +
206T CYS 4.3 0.2 - - - -
234T GLU* 3.2 7.1 - - - +
235T ALA 3.0 40.9 + - - +
237T GLY* 4.6 1.6 - - - -
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Residues in contact with ARG 205 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154T SER 3.8 0.2 - - - +
155T TRP* 3.7 8.7 - - - -
156T TRP* 2.9 74.1 + - + +
159T GLY* 5.2 5.9 + - - -
203T HIS* 3.7 25.8 - - + -
204T PHE* 1.3 75.8 - - - +
206T CYS* 1.3 60.6 + - - +
207T GLN* 2.3 40.2 + - - +
230T ILE* 5.5 0.6 - - - +
232T SER* 4.4 16.8 + - - -
233T ALA 3.4 11.2 - - - +
234T GLU* 4.5 7.0 - - + -
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Residues in contact with CYS 206 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121T VAL* 3.4 4.9 - - + +
123T VAL* 3.6 18.0 - - + +
141T CYS* 2.0 53.4 - - + -
153T LEU* 4.3 17.9 - - - -
154T SER 3.8 4.0 - - - -
155T TRP* 3.8 13.2 - - + -
205T ARG* 1.3 71.2 - - - +
207T GLN* 1.3 60.6 + - - +
208T VAL* 4.7 2.0 - - - -
232T SER* 3.1 6.1 - - - -
233T ALA 2.7 31.3 + - - -
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Residues in contact with GLN 207 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152T GLU 3.8 0.4 - - - +
153T LEU* 3.2 5.2 - - - +
154T SER* 2.8 51.6 + - - +
156T TRP* 3.9 27.2 + - + +
205T ARG* 2.3 47.7 + - - +
206T CYS* 1.3 73.9 - - - +
208T VAL* 1.3 66.6 + - - +
209T GLN* 4.4 2.2 - - - +
230T ILE* 4.2 38.5 - - + +
232T SER* 3.7 4.5 - - - -
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Residues in contact with VAL 208 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119T PRO* 3.7 26.7 - - + -
121T VAL* 3.8 23.3 - - + -
143T ALA* 4.2 14.1 - - + -
151T VAL* 4.0 25.1 - - + -
152T GLU 3.5 4.7 - - - +
153T LEU* 4.2 20.6 - - + -
186T LEU* 5.8 0.7 - - + -
206T CYS* 4.7 2.0 - - - -
207T GLN* 1.3 81.8 - - - +
209T GLN* 1.3 63.8 + - - +
210T PHE* 3.5 2.8 + - - +
230T ILE* 3.6 5.0 - - - -
231T VAL 3.1 34.4 + - - +
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Residues in contact with GLN 209 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150T HIS 3.7 0.7 - - - +
151T VAL* 3.4 6.8 - - - -
152T GLU* 2.9 42.9 + - + +
207T GLN* 4.4 2.6 - - - +
208T VAL* 1.3 71.9 - - - +
210T PHE* 1.3 59.9 + - - +
211T TYR* 3.6 34.7 + - + +
228T THR* 3.8 17.5 - - - +
229T GLN* 3.1 24.5 - - - +
230T ILE* 3.5 25.8 - - + +
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Residues in contact with PHE 210 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116T VAL* 4.1 7.6 - - + -
117T PHE 3.3 12.8 - - - -
118T PRO* 3.8 19.3 - - + -
119T PRO* 3.5 28.9 - - + -
146T PHE* 4.3 2.5 - - + -
147T PHE 3.1 28.7 - - - -
148T PRO* 3.7 12.6 - - + -
150T HIS 3.8 7.9 - - - -
151T VAL* 4.2 7.9 - - + -
208T VAL 3.5 1.0 + - - +
209T GLN* 1.3 71.0 - - - +
211T TYR* 1.3 73.6 + - - +
212T GLY* 3.4 19.7 - - - -
226T PRO 4.0 7.6 - - - -
227T VAL 3.5 16.8 - - - -
228T THR* 3.1 11.1 - - - +
229T GLN* 2.8 39.8 + - + +
231T VAL 5.9 0.2 - - - +
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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