Contacts of the strand formed by residues 115 - 119 (chain D) in PDB entry 1EQB
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 THR 115 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D GLY 4.7 1.2 + - - -
114D ASP* 1.3 73.3 - - - +
116D VAL* 1.3 67.7 + - - +
141D ASN* 3.1 28.9 + - - +
143D VAL* 3.9 24.2 - - + -
165D HIS* 4.3 14.1 + - + +
166D LYS 4.7 1.8 - - - -
167D PRO* 3.9 23.1 - - + -
168D LYS* 2.8 31.2 + - - +
169D MET 3.6 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D TYR* 4.6 5.8 - - + -
110D LEU* 3.4 32.8 - - + -
114D ASP 4.2 7.2 - - - +
115D THR* 1.3 81.2 - - - +
117D LEU* 1.3 64.9 + - - +
118D GLY 3.8 1.1 + - - +
140D TYR* 4.4 10.8 - - + -
141D ASN 2.8 6.1 + - - -
142D ILE* 3.5 21.3 - - + +
143D VAL* 2.9 27.2 + - - +
167D PRO* 4.3 2.7 - - - -
169D MET* 3.4 12.3 - - + +
171D ILE* 3.5 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D VAL* 1.3 72.7 - - - +
118D GLY* 1.3 57.7 + - - +
143D VAL* 3.3 32.8 - - + +
144D PRO 4.4 4.0 - - - +
145D TYR* 3.9 17.0 - - + -
158D LEU* 3.6 32.8 - - + +
161D GLN* 4.2 15.7 - - + -
162D ALA* 4.1 11.0 - - + -
165D HIS* 6.2 0.7 - - + -
167D PRO* 4.0 10.7 - - + +
169D MET 3.0 13.0 + - - +
170D ILE* 3.5 30.6 - - + +
171D ILE 2.7 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D VAL* 3.8 3.0 + - - +
117D LEU* 1.3 74.3 - - - +
119D MET* 1.3 62.5 + - - -
129D HIS* 3.9 17.7 - - - -
142D ILE* 4.6 3.7 - - - +
143D VAL 3.1 6.9 + - - -
144D PRO* 3.2 8.0 - - - +
145D TYR* 3.2 28.2 + - - -
171D ILE* 4.2 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D GLY* 1.3 70.4 - - - -
120D ASN* 1.3 70.8 + - - +
121D LEU 3.6 0.7 + - - -
123D HIS* 3.5 20.4 - - + +
124D GLY 4.0 4.9 - - - -
125D GLY* 3.3 33.9 - - - +
126D HIS 4.7 0.7 - - - +
129D HIS* 3.9 18.9 + - - +
145D TYR* 3.3 39.1 + - + +
146D GLY 4.6 2.7 - - - +
147D ILE* 3.5 24.5 - - + -
153D ILE* 4.2 20.4 - - + -
171D ILE* 4.4 2.0 + - - +
173D GLY 3.8 20.4 - - - +
174D PHE* 4.0 8.3 - - - -
177D TYR* 4.3 11.7 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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