Contacts of the strand formed by residues 192 - 202 (chain D) in PDB entry 1C2O
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 GLY 192 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111D PRO* 4.4 4.5 - - - +
112D THR 3.4 6.7 - - - -
114D VAL* 3.9 10.1 - - - -
145D VAL* 3.7 13.7 - - - -
187D ILE* 3.0 15.3 + - - -
188D ALA* 3.3 13.9 + - - +
190D PHE 3.3 2.2 - - - -
191D GLY* 1.3 81.0 - - - +
193D ASP* 1.3 61.2 + - - -
194D PRO* 3.2 13.3 - - - +
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Residues in contact with ASP 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D PRO* 3.4 30.8 - - + +
112D THR 2.6 21.6 + - - +
113D PRO* 4.4 2.9 - - + -
114D VAL* 4.0 7.2 - - - +
187D ILE* 4.4 2.2 - - - -
192D GLY* 1.3 70.9 - - - -
194D PRO* 1.3 62.7 - - - +
195D MET* 2.8 39.3 + - - +
196D SER* 2.9 31.0 + - - +
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Residues in contact with PRO 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D PRO* 5.5 1.1 - - + -
184D GLN* 3.4 51.1 + - - +
187D ILE* 4.1 12.5 - - + -
188D ALA* 4.5 12.1 - - + -
192D GLY 3.2 11.9 - - - +
193D ASP* 1.3 87.4 - - - +
195D MET* 1.3 66.9 + - + +
196D SER 3.5 0.7 - - - -
197D VAL* 4.1 5.3 - - + +
223D HIS* 3.3 14.6 - - - -
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Residues in contact with MET 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D GLN* 4.9 6.3 - - - +
193D ASP* 2.8 19.4 + - - +
194D PRO* 1.3 93.0 - - + +
196D SER* 1.3 60.0 + - - +
223D HIS* 3.1 36.4 + - - +
224D ARG* 5.4 0.7 + - - -
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Residues in contact with SER 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D PRO* 2.9 30.5 - - - +
114D VAL 2.8 26.0 + - - +
193D ASP* 2.9 20.4 + - - -
195D MET* 1.3 79.8 - - - +
197D VAL* 1.3 59.3 + - - +
198D THR* 3.7 1.1 + - - -
223D HIS* 3.7 1.8 - - - -
224D ARG* 3.5 26.1 + - - +
484D ALA 4.4 0.3 + - - +
485D ARG* 5.0 1.2 - - - -
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Residues in contact with VAL 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D VAL* 3.5 21.1 - - + -
116D ILE* 3.5 22.2 - - + -
183D VAL* 4.2 10.3 - - + -
184D GLN* 4.0 15.5 - - - +
194D PRO* 4.1 14.1 - - + +
196D SER* 1.3 74.1 - - - +
198D THR* 1.3 61.7 + - - +
199D LEU* 4.3 4.5 - - + -
221D LEU 3.0 28.9 - - - +
222D PHE* 3.3 16.1 - - + -
223D HIS* 2.7 35.9 + - - +
224D ARG 3.2 5.7 + - - +
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Residues in contact with THR 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D VAL 2.8 9.8 + - - -
115D LEU* 3.5 30.6 - - + +
116D ILE 3.3 19.5 + - - -
196D SER 3.7 1.0 + - - -
197D VAL* 1.3 72.2 - - - +
199D LEU* 1.3 67.9 + - - +
200D PHE* 3.7 2.2 + - + -
224D ARG* 2.9 43.5 + - + +
226D VAL* 4.3 16.8 - - + -
480D TRP* 5.6 1.3 - - + +
483D PHE* 4.7 1.8 - - + -
484D ALA* 3.7 15.9 + - + -
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Residues in contact with LEU 199 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D ILE* 3.5 20.0 - - + +
118D ILE* 4.8 5.6 - - + -
180D LEU* 3.4 34.8 - - + -
197D VAL 4.0 0.2 - - - -
198D THR* 1.3 75.2 - - - +
200D PHE* 1.3 61.1 + - - +
209D VAL* 4.0 25.4 - - + -
212D HIS* 3.9 28.7 - - + +
222D PHE* 3.5 44.4 - - + -
224D ARG 3.1 8.0 + - - +
225D ALA* 3.4 1.2 - - - -
226D VAL* 2.9 24.6 + - - +
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Residues in contact with PHE 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D LEU* 3.9 39.3 - - + -
116D ILE 2.9 19.0 + - - -
117D TRP* 2.9 53.6 - + + -
118D ILE* 3.0 14.1 + - - +
138D LEU* 5.0 3.4 - - + -
146D LEU* 4.8 4.0 - - + -
198D THR* 4.6 1.3 - - + +
199D LEU* 1.3 79.0 - - - +
201D GLY* 1.3 58.3 + - - +
209D VAL* 4.1 2.7 - - - +
226D VAL* 3.5 26.0 - - + -
228D GLN* 3.6 17.3 - - - -
454D ILE* 4.1 17.5 - - + -
455D PHE* 3.5 31.4 - + - -
480D TRP* 4.0 14.6 - + - -
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Residues in contact with GLY 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D TRP* 3.6 9.0 - - - -
118D ILE 3.4 16.4 - - - -
200D PHE* 1.3 76.4 - - - +
202D GLU* 1.3 59.0 + - - -
205D GLY 4.0 2.0 - - - -
206D ALA* 3.1 18.3 - - - +
209D VAL* 3.7 8.4 - - - +
226D VAL 3.7 2.8 + - - -
227D LEU 3.7 0.2 - - - -
228D GLN* 2.9 27.8 + - - +
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Residues in contact with GLU 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D TRP* 6.3 0.2 - - - -
117D TRP* 3.7 13.6 - - + -
118D ILE 3.9 2.4 + - - -
120D GLY* 3.9 10.6 + - - +
133D TYR* 5.5 1.8 + - - +
201D GLY* 1.3 73.1 - - - -
203D SER* 1.3 98.7 + - - +
204D ALA 3.1 0.2 + - - -
205D GLY* 2.6 19.2 + - - -
206D ALA 2.7 4.2 + - - -
228D GLN* 3.1 17.7 - - + +
229D SER* 4.0 2.9 - - - -
447D HIS* 3.7 12.3 + - - -
448D GLY* 3.0 31.3 + - - -
450D GLU* 3.4 20.9 - - - +
451D ILE* 3.5 27.1 - - + +
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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