Contacts of the strand formed by residues 111 - 116 (chain D) in PDB entry 1EJH
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 111 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D GLY* 1.3 74.2 - - - -
112D ARG* 1.3 60.6 + - - -
166D TRP* 3.3 4.9 - - - -
167D THR 2.8 27.8 + - - -
197D TYR* 2.7 21.8 + - - -
198D GLN 3.0 13.7 - - - -
199D SER* 3.7 3.1 - - - -
200D HIS* 3.5 13.7 + - - -
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Residues in contact with ARG 112 (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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102D TRP* 5.7 4.0 - - - +
111D GLY* 1.3 75.3 - - - +
113D TRP* 1.3 59.7 + - - +
114D LEU* 3.6 27.8 + - + +
153D VAL* 6.2 1.0 - - - +
155D ASN* 4.1 17.6 + - - -
162D LYS* 4.5 11.3 - - - +
164D ALA* 4.0 18.8 - - + +
165D ILE 3.4 4.5 - - - -
166D TRP* 3.7 33.0 - - + +
196D GLY 3.6 0.7 - - - +
197D TYR* 3.1 10.0 - - - -
198D GLN* 2.7 65.3 + - - +
200D HIS* 3.8 17.5 - - + -
203D THR* 4.5 21.0 - - - +
1004D M7G 4.7 10.3 + - - -
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Residues in contact with TRP 113 (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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112D ARG* 1.3 69.9 - - - +
114D LEU* 1.3 59.9 + - - +
115D ILE* 3.9 4.0 + - - +
163D ILE 3.8 1.2 - - - +
164D ALA* 3.0 23.9 - - - -
165D ILE* 3.0 17.6 + - + +
167D THR* 4.7 0.9 - - + -
176D VAL* 2.9 42.1 + - + +
177D THR* 4.5 1.1 - - - -
179D ILE* 3.7 23.4 - - + +
180D GLY* 3.2 19.1 - - - +
183D TYR* 4.6 14.7 - + + -
195D ILE* 3.2 41.5 - - + -
196D GLY* 3.2 32.3 - - - -
197D TYR* 3.5 29.3 - + + -
215D PHE* 3.9 14.6 - - + -
216D VAL 3.9 2.2 - - - -
217D VAL* 3.6 23.8 - - + -
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Residues in contact with LEU 114 (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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112D ARG* 3.6 35.6 + - + +
113D TRP* 1.3 72.1 - - - +
115D ILE* 1.3 76.5 + - - +
116D THR* 3.1 28.5 + - - +
162D LYS* 4.1 17.9 - - + +
163D ILE 4.1 1.3 - - - -
164D ALA* 4.2 4.3 - - + -
195D ILE* 4.1 11.1 - - - +
196D GLY 3.0 17.5 + - - +
198D GLN* 3.4 31.2 - - - +
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Residues in contact with ILE 115 (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 TRP 4.5 1.3 - - - +
114D LEU* 1.3 78.5 - - - +
116D THR* 1.3 62.5 + - - +
117D LEU* 3.8 24.2 + - + +
129D PHE* 5.2 1.1 - - + -
162D LYS* 3.3 4.7 - - - -
163D ILE* 2.9 45.2 + - + +
183D TYR* 3.8 24.2 - - + +
187D LEU* 4.0 10.5 - - + -
189D LEU* 3.8 21.8 - - + -
195D ILE* 3.3 46.9 - - + -
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Residues in contact with THR 116 (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 LEU* 3.1 21.5 + - - +
115D ILE* 1.3 76.5 - - - +
117D LEU* 1.3 77.2 + - - +
160D GLY* 4.8 6.5 - - - +
161D ASP 3.7 9.0 - - - +
162D LYS* 3.6 12.5 - - + +
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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