Contacts of the strand formed by residues 192 - 201 (chain D) in PDB entry 3CB4
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 GLN 192 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190D PRO* 3.5 4.9 + - - +
191D LEU* 1.3 79.2 - - - +
193D ALA* 1.3 60.0 + - - +
194D LEU 4.2 0.7 - - - -
212D ILE* 3.8 1.0 - - - -
213D LYS* 2.9 30.9 + - + +
214D ASN* 2.8 36.9 + - - +
273D THR* 5.1 5.6 - - - +
274D LEU 3.5 2.5 - - - -
281D ALA* 3.8 14.6 - - + +
283D LYS* 2.8 29.1 + - - +
284D ALA* 4.5 0.6 - - - +
285D LEU* 4.1 37.4 - - + +
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Residues in contact with ALA 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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191D LEU* 4.1 13.9 - - + -
192D GLN* 1.3 72.1 - - - +
194D LEU* 1.3 64.3 + - - +
195D ILE* 3.4 3.1 + - - +
210D ILE* 3.7 28.0 - - + +
211D ARG 3.3 4.9 - - - +
212D ILE* 4.2 4.5 - - + -
217D LEU* 5.4 2.0 - - + -
273D THR* 3.3 4.9 - - - -
274D LEU* 2.8 53.4 + - + +
285D LEU* 4.3 1.2 - - - +
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Residues in contact with LEU 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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90D ARG* 3.7 33.9 - - - +
93D ALA* 3.8 21.5 - - + +
94D ALA* 3.9 15.9 - - + +
193D ALA* 1.3 70.3 - - - +
195D ILE* 1.3 73.9 + - - +
196D ILE* 3.2 8.9 + - + +
210D ILE* 3.4 3.2 - - - -
211D ARG* 2.9 40.6 + - + +
213D LYS* 4.5 9.0 - - + -
271D GLY* 3.7 26.9 - - - +
272D ASP 3.6 3.8 - - - +
285D LEU* 3.8 24.0 - - + +
286D PRO 6.0 0.2 - - - +
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Residues in contact with ILE 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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90D ARG* 4.7 1.0 - - - +
193D ALA 3.9 1.3 - - - +
194D LEU* 1.3 73.3 - - - +
196D ILE* 1.3 61.7 + - - +
197D ASP 3.9 9.2 - - - +
198D SER* 3.5 23.6 - - - +
208D SER* 4.6 9.4 - - - +
209D LEU 3.6 7.6 - - - +
210D ILE* 4.9 2.0 - - + -
225D VAL* 5.2 2.0 - - + -
268D ALA* 3.9 7.9 - - + +
269D PRO 3.5 18.6 - - - +
270D VAL* 3.8 8.8 - - - +
271D GLY* 2.9 28.1 + - - -
272D ASP* 3.1 40.8 + - + +
273D THR 3.8 1.8 - - - +
274D LEU* 3.7 38.6 - - + -
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Residues in contact with ILE 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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57D GLN* 5.7 0.2 - - - +
76D ILE* 4.4 10.5 - - + -
87D GLU* 5.0 2.3 - - - +
90D ARG* 4.6 8.1 - - - +
91D SER* 3.4 32.8 + - - +
94D ALA* 3.9 20.4 - - + -
194D LEU* 3.9 10.5 - - + +
195D ILE* 1.3 72.8 - - - +
197D ASP* 1.3 64.7 + - + +
209D LEU* 3.1 31.3 + - + +
210D ILE 3.5 14.1 - - - +
211D ARG* 3.5 34.5 - - + +
255D VAL* 4.4 7.9 - - + -
270D VAL* 3.4 20.1 - - - +
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Residues in contact with ASP 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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57D GLN* 3.0 33.4 + - - +
87D GLU* 5.4 7.9 - - - +
195D ILE* 3.5 4.3 - - - +
196D ILE* 1.3 84.6 - - + +
198D SER* 1.3 80.1 + - - +
199D TRP* 4.1 11.6 - - + +
208D SER* 3.3 0.9 - - - -
209D LEU* 2.7 36.2 + - + +
270D VAL* 4.7 8.6 - - - +
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Residues in contact with SER 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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195D ILE* 3.5 4.2 - - - +
197D ASP* 1.3 85.6 + - - +
199D TRP* 1.3 65.4 + - - +
206D VAL* 4.9 1.1 - - - -
207D VAL 3.3 7.4 - - - -
208D SER* 2.9 22.9 + - - -
265D ILE* 3.7 27.4 - - - +
268D ALA* 2.9 30.7 + - - +
270D VAL* 5.3 3.4 - - - +
320D ASN 4.8 3.8 - - - +
322D ALA* 6.1 0.3 - - - +
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Residues in contact with TRP 199 (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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57D GLN* 3.8 30.1 - - - -
197D ASP* 3.9 9.4 - - - +
198D SER* 1.3 82.6 - - - +
200D PHE* 1.3 74.0 + - - +
201D ASP* 4.5 6.8 + - + +
206D VAL* 3.4 3.1 - - - -
207D VAL* 2.8 64.8 + - + +
208D SER 4.2 2.9 - - - -
209D LEU* 3.8 46.4 - - + -
240D PHE* 4.1 21.3 - + - -
265D ILE* 3.6 11.6 - - - +
320D ASN* 3.6 15.3 - - - +
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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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199D TRP* 1.3 81.8 - - - +
201D ASP* 1.3 76.4 + - - +
202D ASN* 4.2 20.1 + - - +
205D GLY* 3.8 15.7 - - - -
206D VAL* 3.8 24.5 - - + -
263D LYS 4.5 9.0 - - - -
264D ASP* 5.7 1.1 - - - -
265D ILE* 4.1 1.7 - - + +
319D LEU* 3.6 51.4 - - + +
320D ASN* 3.1 22.3 + - - +
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Residues in contact with ASP 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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199D TRP* 4.8 6.8 + - + -
200D PHE* 1.3 80.8 - - - +
202D ASN* 1.3 62.9 + - - +
203D TYR* 2.8 32.4 + - - +
204D LEU* 2.8 35.6 + - + +
205D GLY* 2.7 45.7 + - - +
207D VAL* 3.8 9.4 - - + +
244D GLN* 5.3 3.3 + - - -
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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