Contacts of the strand formed by residues 116 - 121 (chain D) in PDB entry 4CEV
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 116 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106D LEU* 3.9 25.1 - - + -
109D VAL* 3.9 12.6 - - + -
110D ALA* 3.7 35.7 - - + +
113D TYR* 4.0 24.2 + - + +
114D GLU 4.1 0.2 - - - -
115D ARG* 1.3 74.1 - - - +
117D GLY* 1.3 68.9 + - - +
118D VAL 4.2 0.2 + - - -
163D LYS 4.9 2.6 + - - +
164D ILE* 3.6 25.0 - - + +
168D HIS* 3.7 12.5 + - - +
218D THR* 4.2 0.7 - - - -
219D ASP* 3.6 2.4 + - - -
220D GLY* 3.3 30.5 - - - +
221D VAL 3.9 2.9 - - - +
222D HIS* 3.9 8.1 - - + +
265D THR* 4.2 4.0 - - - +
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Residues in contact with GLY 117 (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 ARG 3.4 3.2 + - - -
116D LEU* 1.3 76.9 - - - +
118D VAL* 1.3 66.1 + - - +
168D HIS 3.2 11.9 - - - -
214D LEU* 4.2 3.8 - - - -
218D THR* 3.5 16.6 - - - +
220D GLY 2.7 13.5 + - - -
221D VAL* 3.4 8.0 - - - -
222D HIS 2.9 24.0 + - - -
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Residues in contact with VAL 118 (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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106D LEU* 4.0 13.7 - - + -
117D GLY* 1.3 79.5 - - - +
119D ILE* 1.3 70.0 + - - +
120D TRP* 3.8 33.6 + - + +
143D LEU* 4.6 5.6 - - + -
164D ILE* 3.6 37.9 - - + -
168D HIS 2.9 9.8 + - - +
169D VAL* 3.5 11.7 - - + -
170D VAL* 2.9 27.7 + - - +
214D LEU* 4.3 2.7 - - - +
221D VAL* 4.4 0.2 - - - +
222D HIS* 3.4 16.6 - - + +
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Residues in contact with ILE 119 (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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118D VAL* 1.3 71.9 - - - +
120D TRP* 1.3 59.0 - - - +
121D TYR* 4.5 9.9 - - + +
170D VAL* 3.3 4.5 - - + +
172D ILE* 4.0 24.5 - - + -
207D MET* 5.2 1.8 - - + -
210D THR* 3.9 18.4 - - + -
214D LEU* 3.4 25.4 - - + -
221D VAL* 4.0 12.8 - - + +
222D HIS 3.0 8.3 + - - +
223D LEU* 3.7 20.0 - - + +
224D SER* 2.9 28.4 + - - +
258D LEU* 3.8 33.0 - - + -
263D ILE* 4.8 3.1 - - + -
264D ILE* 4.1 5.2 - - + -
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Residues in contact with TRP 120 (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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99D HIS* 3.2 22.7 - + - -
102D ALA* 3.5 26.7 - - + -
106D LEU* 4.3 14.1 - - + -
118D VAL* 3.8 10.7 - - + -
119D ILE* 1.3 70.9 - - - +
121D TYR* 1.3 63.5 + - - +
122D ASP* 3.1 29.3 + - + +
124D HIS 4.0 1.8 - - - -
125D GLY 4.2 1.1 - - - -
126D ASP* 2.9 34.3 + - + +
142D PRO* 3.7 10.5 - - + -
143D LEU* 3.7 46.0 - - + -
169D VAL* 5.1 1.1 - - + -
170D VAL 2.8 10.6 + - - +
171D LEU* 3.4 31.3 - - + +
172D ILE 3.0 23.9 + - - -
224D SER* 3.5 26.7 - - - -
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Residues in contact with TYR 121 (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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119D ILE* 3.7 6.7 + - + +
120D TRP* 1.3 69.0 - - - +
122D ASP* 1.3 59.6 + - - +
172D ILE* 3.5 29.8 - - + -
203D MET* 3.6 9.4 - - + +
207D MET* 5.3 0.7 - - - -
223D LEU* 4.7 6.1 - - + -
224D SER 3.1 9.6 + - - +
225D LEU* 3.6 40.4 - - + -
226D ASP* 2.9 32.5 + - - +
229D GLY* 4.8 2.7 - - - -
230D LEU* 4.2 10.5 - - + -
246D LEU* 3.3 30.5 - - + +
251D SER* 2.9 43.4 + - - -
254D ALA* 4.1 18.8 - - + -
255D MET* 4.5 7.0 - - + -
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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