Contacts of the strand formed by residues 169 - 173 (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 MET 169 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D VAL* 3.9 17.9 - - + +
106D TYR* 4.9 5.8 - - - -
109D LEU* 3.5 42.2 - - + -
110D LEU* 3.9 29.6 - - + -
115D THR 3.6 1.8 + - - -
116D VAL* 3.4 9.2 - - + +
117D LEU 3.0 23.7 + - - -
167D PRO* 3.2 5.1 + - - +
168D LYS* 1.3 82.4 - - - +
170D ILE* 1.3 70.1 + - - +
171D ILE* 4.4 9.4 - - + -
195D ALA* 4.3 0.2 - - - -
196D TYR* 3.4 18.2 - - + +
198D PHE* 3.8 31.6 - - + -
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Residues in contact with ILE 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D LEU* 3.5 37.9 - - + +
145D TYR* 4.9 1.6 - - + -
158D LEU* 5.0 3.8 - - + -
162D ALA* 4.1 7.0 - - + -
167D PRO* 3.9 10.3 - - + -
169D MET* 1.3 79.2 - - - +
171D ILE* 1.3 63.5 + - - +
186D MET* 3.9 28.3 - - + +
189D ILE* 4.0 25.8 - - + -
190D ALA* 4.1 18.8 - - + +
193D ILE* 4.5 2.9 - - + -
195D ALA* 4.4 4.7 - - + -
196D TYR 2.7 13.2 + - - +
197D LEU* 3.5 11.4 - - + +
198D PHE* 2.9 25.3 + - - +
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Residues in contact with ILE 171 (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 TYR* 3.1 33.4 - - + +
116D VAL* 3.5 27.4 - - + -
117D LEU 2.7 12.6 + - - +
118D GLY* 4.2 6.5 - - - -
119D MET* 4.4 1.7 + - - +
128D THR 4.7 0.2 - - - +
129D HIS* 4.0 40.8 - - + +
145D TYR* 2.7 34.1 + - - -
169D MET* 4.4 3.6 - - - -
170D ILE* 1.3 74.1 - - - +
172D GLY* 1.3 62.1 + - - +
173D GLY 4.3 0.3 + - - +
186D MET* 3.9 3.1 - - - +
198D PHE* 3.2 31.4 - - + +
200D ASP* 5.1 0.9 - - + -
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Residues in contact with GLY 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D TYR* 3.8 1.8 - - - -
170D ILE 3.9 1.0 + - - -
171D ILE* 1.3 78.7 - - - +
173D GLY* 1.3 58.8 + - - -
181D VAL* 5.6 0.2 - - - -
183D TRP* 4.1 7.2 - - - -
186D MET* 3.8 25.5 - - - +
197D LEU* 4.6 1.0 - - - +
198D PHE 2.8 9.6 + - - +
199D VAL* 3.1 12.8 - - - +
200D ASP* 2.8 25.1 + - - -
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Residues in contact with GLY 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D MET* 3.8 17.5 - - - +
129D HIS* 3.9 16.2 + - - -
145D TYR* 4.5 1.7 + - - -
171D ILE 5.2 0.2 - - - +
172D GLY* 1.3 74.8 - - - -
174D PHE* 1.3 77.3 + - - +
181D VAL* 5.5 1.8 - - - +
183D TRP* 4.3 11.1 - - - -
200D ASP 3.4 16.6 - - - -
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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