Contacts of the strand formed by residues 196 - 201 (chain D) in PDB entry 4C3P
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 LEU 196 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D VAL* 3.8 46.9 - - + +
185D GLN* 4.0 25.2 + - + +
186D SER* 3.6 30.7 - - - +
194D LEU 3.5 2.8 + - - -
195D ARG* 1.3 81.6 + - - +
197D TYR* 1.3 58.6 - - - +
198D GLY 3.4 26.7 - - - +
208D LEU* 3.7 11.9 - - + -
209D ILE 3.4 16.6 - - - +
210D LEU* 3.6 22.4 - - + -
13E PRO* 5.7 0.2 - - - +
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Residues in contact with TYR 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D TRP* 4.8 2.9 + - + -
157D PHE* 4.1 27.8 - + - -
159D LEU* 5.3 1.6 - - + -
195D ARG* 3.4 54.4 + - + +
196D LEU* 1.3 72.8 - - - +
198D GLY* 1.3 55.6 + - - +
209D ILE* 2.6 34.3 + - + +
210D LEU 4.3 3.1 - - - -
211D GLU* 4.0 32.0 + - - +
13E PRO* 3.9 17.6 - - - +
17E ILE* 3.9 27.6 - - + +
19E PHE* 4.5 24.2 - + + -
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Residues in contact with GLY 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D TRP* 4.1 11.7 - - - -
186D SER* 5.7 0.4 - - - -
196D LEU* 3.4 13.7 - - - +
197D TYR* 1.3 82.4 - - - +
199D TYR* 1.3 62.7 + - - +
209D ILE* 3.0 30.8 + - - +
12E ALA* 6.3 0.4 - - - -
13E PRO* 3.3 17.5 - - - -
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Residues in contact with TYR 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D TRP* 3.7 4.1 - - - -
182D VAL* 4.6 4.9 - - + -
198D GLY* 1.3 75.5 - - - +
200D PHE* 1.3 77.5 - - - +
201D HIS* 3.8 18.0 + + - -
206D VAL* 4.4 8.7 - - + -
207D TYR 3.3 14.1 - - - +
208D LEU* 4.0 12.6 - - + +
209D ILE* 4.7 0.2 - - - -
8E TYR* 2.6 28.7 + - + -
9E SER* 3.6 2.1 - - - -
10E TYR* 3.0 53.5 + + + -
12E ALA* 3.7 26.5 - - + -
13E PRO 3.1 14.5 + - - -
14E SER* 2.7 39.8 + - - -
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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
----------------------------------------------------------
128D TRP* 3.2 39.9 - + + +
129D ALA* 4.0 3.4 - - - -
130D LEU* 3.6 26.0 - - + -
133D PHE* 3.7 33.0 - + - -
161D LEU* 4.9 1.8 - - + -
199D TYR* 1.3 84.6 - - - +
201D HIS* 1.3 73.1 + - - +
202D ASP* 6.0 0.7 - - + -
206D VAL* 3.9 3.3 - - - +
207D TYR* 3.0 67.6 + + + +
209D ILE* 3.8 12.8 - - + -
14E SER* 4.1 7.0 - - - +
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Residues in contact with HIS 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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166D LYS* 3.1 28.5 + - - -
199D TYR* 3.8 16.0 + + - -
200D PHE* 1.3 84.3 - - - +
202D ASP* 1.3 60.7 + - - +
205D ARG 3.4 14.4 - - - +
206D VAL* 4.3 9.2 - - + -
207D TYR* 4.2 2.7 - - - -
7E SER 3.6 19.2 + - - -
8E TYR* 3.5 28.4 + - + -
9E SER* 5.4 0.8 + - - -
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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