Contacts of the strand formed by residues 198 - 208 (chain A) in PDB entry 1IS2
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 GLU 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A ILE* 3.4 8.0 - - - +
195A THR 3.1 25.5 + - - +
196A GLN* 3.4 14.3 - - + +
197A GLY* 1.3 88.2 - - - +
199A CYS* 1.3 61.3 + - - +
200A TYR* 3.3 37.9 - - + +
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Residues in contact with CYS 199 (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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192A GLN* 4.0 30.5 - - - -
193A LEU 3.3 6.7 - - - -
194A ILE* 4.3 12.6 - - + -
198A GLU* 1.3 74.6 - - - +
200A TYR* 1.3 65.4 + - - +
201A GLY* 3.8 12.4 + - - -
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Residues in contact with TYR 200 (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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193A LEU* 2.8 18.5 + - + +
195A THR* 3.5 33.0 + - + +
196A GLN* 4.8 7.4 + - - -
198A GLU* 3.3 43.0 - - + +
199A CYS* 1.3 74.4 - - - +
201A GLY* 1.3 59.7 + - - +
203A HIS* 3.3 15.1 + - - +
265A TYR* 3.2 60.1 + + + +
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Residues in contact with GLY 201 (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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192A GLN* 3.5 16.2 - - - -
193A LEU 2.9 22.9 + - - -
199A CYS* 3.5 10.9 + - - -
200A TYR* 1.3 78.2 - - - +
202A LEU* 1.3 62.4 + - - -
203A HIS* 3.0 9.7 - - - -
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Residues in contact with LEU 202 (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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147A LEU* 3.9 26.7 - - + +
148A ARG* 4.3 6.1 - - - -
150A LEU* 3.9 21.5 - - + -
190A LEU* 3.6 28.4 - - + +
191A ALA* 3.3 17.9 - - - +
192A GLN* 3.3 30.5 - - + +
201A GLY* 1.3 72.4 - - - -
203A HIS* 1.3 69.0 + - - +
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Residues in contact with HIS 203 (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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190A LEU* 3.4 7.9 - - - -
191A ALA 2.9 29.5 + - - -
193A LEU* 3.4 22.3 - - + +
200A TYR 3.3 12.9 + - - -
201A GLY 3.0 25.6 - - - -
202A LEU* 1.3 79.7 + - - +
204A ALA* 1.3 62.7 + - - +
205A PHE* 3.1 26.5 - - + -
252A MET* 4.3 7.7 - - + +
253A LEU 5.3 2.6 + - - +
257A ALA* 3.3 21.6 - - + +
265A TYR* 3.0 36.4 + + - -
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Residues in contact with ALA 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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110A THR* 5.7 1.1 - - + -
114A GLN* 5.5 2.9 - - - +
136A TYR* 5.2 3.4 - - + -
188A ILE* 3.9 13.0 - - + -
189A VAL 3.5 5.6 - - - +
190A LEU* 4.4 10.3 - - + +
203A HIS* 1.3 72.2 - - - +
205A PHE* 1.3 69.1 + - - +
252A MET* 3.7 4.3 - - - +
253A LEU* 3.1 52.6 + - + +
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Residues in contact with PHE 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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154A ALA* 3.4 26.9 - - + -
163A PHE* 3.7 35.9 - + - -
165A LEU* 4.7 8.5 - - + -
188A ILE* 3.3 4.6 - - - -
189A VAL* 2.9 39.5 + - + +
191A ALA* 4.2 10.3 - - + -
193A LEU* 4.3 13.5 - - + -
203A HIS* 3.1 41.5 - - + -
204A ALA* 1.3 75.7 - - - +
206A VAL* 1.3 65.3 + - - +
207A VAL* 3.4 3.0 + - + +
247A ILE* 3.9 19.7 - - + -
251A ASN 3.6 4.3 - - - +
252A MET* 3.7 27.8 - - + -
253A LEU* 4.7 0.7 - - - +
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Residues in contact with VAL 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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107A PHE* 5.0 10.1 - - + -
111A LEU* 4.2 11.2 - - + -
119A GLN* 5.2 1.1 - - - +
123A PHE* 3.5 57.0 - - + -
186A HIS* 4.3 10.1 - - + -
187A ALA 4.1 1.8 - - - -
188A ILE* 4.5 9.4 - - + +
205A PHE* 1.3 73.3 - - - +
207A VAL* 1.3 61.3 + - - +
247A ILE* 3.7 4.7 - - - +
251A ASN* 2.8 45.8 + - + +
253A LEU* 4.1 20.4 - - + -
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Residues in contact with VAL 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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165A LEU* 5.1 4.5 - - + -
186A HIS* 4.5 2.5 - - - -
187A ALA* 2.8 45.7 + - + +
189A VAL* 3.1 31.4 - - + -
205A PHE* 3.9 2.5 - - + +
206A VAL* 1.3 78.1 - - - +
208A PRO* 1.3 78.6 - - + +
209A ILE* 3.4 11.4 + - + +
221A ILE* 4.6 0.7 - - + -
242A MET* 4.6 11.7 - - - -
245A TYR* 3.4 24.9 - - + -
247A ILE* 4.2 10.8 - - + -
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Residues in contact with PRO 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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123A PHE* 5.4 1.6 - - + -
185A ASN 3.6 7.9 - - - +
186A HIS* 3.7 26.9 - - + +
206A VAL* 4.0 6.1 - - + +
207A VAL* 1.3 85.3 - - + +
209A ILE* 1.3 56.4 + - - +
210A ARG 3.8 1.1 - - - +
218A LEU* 3.8 9.0 - - + -
245A TYR* 2.6 44.9 + - + +
247A ILE* 4.2 8.1 - - + -
248A PRO* 6.2 1.8 - - + -
251A ASN* 4.1 13.5 - - - +
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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