Contacts of the strand formed by residues 196 - 202 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159H ARG* 3.4 2.3 - - - -
160H ASN* 2.5 57.5 + - - +
161H GLY 6.0 0.7 - - - +
195H GLU* 1.3 76.2 - - - +
197H TYR* 1.3 62.1 + - - +
198H THR* 4.6 2.2 - - - +
213H GLU* 3.1 35.0 - - + +
215H LYS* 3.5 26.9 - - + -
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Residues in contact with TYR 197 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141H LEU* 3.5 24.0 - - + -
157H TRP* 4.0 6.7 - - + -
158H PHE 3.1 5.6 - - - +
159H ARG* 2.9 60.2 + - + -
187H LEU* 4.1 14.1 - - + -
189H THR* 3.7 23.6 + - - -
190H VAL 4.1 6.8 + - - -
191H PRO* 4.2 8.1 - - + +
195H GLU* 3.3 27.5 + - + +
196H VAL* 1.3 76.8 - - - +
198H THR* 1.3 62.5 + - - +
212H VAL 4.0 0.2 - - - +
213H GLU* 3.1 4.5 - - - +
214H TRP* 2.7 70.4 + + + +
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Residues in contact with THR 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H TRP* 3.1 9.8 - - - -
158H PHE* 2.6 57.9 + - + +
196H VAL* 4.6 3.6 + - - +
197H TYR* 1.3 73.9 + - - +
199H CYS* 1.3 65.5 + - - +
200H GLN 4.5 0.9 - - - +
211H THR* 3.9 29.8 - - + -
212H VAL 3.5 12.8 - - - +
213H GLU* 3.0 27.9 - - + +
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Residues in contact with CYS 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H VAL* 5.2 0.6 - - + +
127H VAL* 4.0 15.7 - - + -
143H CYS* 2.0 52.3 - - + -
155H VAL* 3.2 23.3 - - - -
156H ARG 3.4 6.7 - - - -
157H TRP* 4.1 8.1 - - + -
198H THR* 1.3 79.5 - - - +
200H GLN* 1.3 57.8 + - - +
201H VAL* 3.9 6.5 + - - +
210H VAL 3.6 1.6 - - - +
211H THR* 3.4 4.3 - - - -
212H VAL* 3.1 25.4 + - + +
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Residues in contact with GLN 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154H GLU 3.4 1.7 - - - +
155H VAL* 3.3 4.9 - - - -
156H ARG* 2.8 68.9 + - + +
158H PHE* 3.4 31.7 - - + -
198H THR* 4.0 2.7 - - + -
199H CYS* 1.3 70.9 - - - +
201H VAL* 1.3 63.9 + - - +
202H GLU* 4.2 14.3 + - + +
209H PRO* 4.1 24.1 - - + +
210H VAL 3.6 2.9 - - - -
211H THR* 4.0 19.8 - - + +
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Residues in contact with VAL 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123H PRO* 4.5 7.2 - - + -
125H VAL* 3.9 36.1 - - + -
145H VAL* 4.1 15.9 - - + -
153H ILE* 3.7 33.2 - - + -
154H GLU 3.3 3.4 - - - +
155H VAL* 4.2 4.7 - - + -
199H CYS* 4.2 11.2 - - - +
200H GLN* 1.3 78.2 - - - +
202H GLU* 1.3 65.5 + - - +
206H LEU* 3.5 9.8 - - + +
209H PRO* 3.6 2.3 - - - +
210H VAL* 2.9 39.0 + - + +
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Residues in contact with GLU 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153H ILE* 3.4 4.2 - - - +
154H GLU* 2.8 68.6 + - + +
156H ARG* 3.4 20.8 + - - -
200H GLN* 4.2 14.4 + - + +
201H VAL* 1.3 72.7 - - - +
203H HIS* 1.3 64.3 + - - +
209H PRO* 3.7 30.4 - - + +
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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