Contacts of the strand formed by residues 196 - 202 (chain B) in PDB entry 1I3R
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 VAL 196 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B PHE 4.0 0.2 - - - +
159B ARG* 3.6 0.9 - - - -
160B ASN* 2.6 54.5 + - - +
161B GLY 4.8 0.3 + - - -
195B GLU* 1.3 78.9 - - - +
197B TYR* 1.3 62.2 + - - +
198B THR* 4.8 3.7 + - + +
213B GLU* 3.3 35.4 - - + +
214B TRP 3.8 1.8 - - - -
215B LYS* 3.5 29.8 - - + +
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Residues in contact with TYR 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 3.2 32.8 - - + -
157B TRP* 4.4 3.4 - - + -
158B PHE 3.2 14.4 - - - +
159B ARG* 3.2 41.4 + - + -
187B LEU* 4.2 16.2 - - + -
189B THR* 3.1 37.2 - - + +
190B VAL 4.3 1.7 + - - -
191B PRO* 4.4 4.9 - - + -
195B GLU* 3.1 35.5 + - + -
196B VAL* 1.3 74.1 - - - +
198B THR* 1.3 67.2 + - - +
213B GLU* 3.6 0.7 - - - +
214B TRP* 2.6 61.9 + + + +
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Residues in contact with THR 198 (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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156B ARG 3.8 0.9 - - - +
157B TRP* 3.3 10.1 - - - -
158B PHE* 2.8 66.8 + - - +
160B ASN 5.8 0.2 + - - -
161B GLY 5.6 1.2 + - - -
196B VAL* 4.8 3.5 + - + -
197B TYR* 1.3 85.7 - - - +
199B CYS* 1.3 62.1 + - - +
200B GLN* 4.0 0.6 + - - -
211B THR* 5.2 7.6 - - - -
212B VAL 3.2 8.1 - - - +
213B GLU* 3.3 35.7 - - + +
214B TRP* 5.9 0.2 - - - -
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Residues in contact with CYS 199 (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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125B VAL* 5.0 0.4 - - + +
127B VAL* 4.0 14.6 - - + -
143B CYS* 2.0 52.5 - - + -
155B VAL* 3.4 22.7 - - - -
156B ARG 3.5 4.3 - - - -
157B TRP* 4.1 8.9 - - + -
198B THR* 1.3 72.9 - - - +
200B GLN* 1.3 59.1 + - - +
201B VAL* 3.9 7.8 + - - +
210B VAL 3.5 1.9 - - - +
211B THR* 3.2 5.9 - - - -
212B VAL* 2.9 32.4 + - + +
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Residues in contact with GLN 200 (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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154B GLU 3.5 1.7 - - - +
155B VAL* 3.4 4.0 - - - +
156B ARG* 2.8 74.6 + - + +
158B PHE* 3.8 30.1 - - + -
198B THR 4.0 1.0 + - - -
199B CYS* 1.3 72.9 - - - +
201B VAL* 1.3 62.8 + - - +
202B GLU* 4.2 15.0 + - + -
209B PRO* 4.2 27.5 - - + +
210B VAL 3.5 3.6 - - - -
211B THR* 4.0 16.1 - - + +
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B PRO* 4.3 10.8 - - + -
125B VAL* 3.6 33.7 - - + -
145B VAL* 3.8 18.2 - - + -
153B ILE* 3.8 30.7 - - + -
154B GLU 3.5 2.9 - - - +
155B VAL* 4.3 5.4 - - + -
199B CYS* 4.2 14.4 - - - +
200B GLN* 1.3 78.1 - - - +
202B GLU* 1.3 65.8 + - - +
206B LEU* 3.4 9.0 - - + +
209B PRO* 3.7 1.1 - - - +
210B VAL* 2.7 36.9 + - + +
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Residues in contact with GLU 202 (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 ASN 4.6 0.2 - - - +
153B ILE* 3.4 5.2 - - - +
154B GLU* 2.9 74.9 + - + +
156B ARG* 3.6 12.8 + - - +
200B GLN* 4.2 17.1 + - + -
201B VAL* 1.3 74.6 - - - +
203B HIS* 1.3 64.8 + - - +
206B LEU* 4.8 0.4 - - - -
209B PRO* 4.0 27.7 - - + +
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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