Contacts of the strand formed by residues 161 - 170 (chain B) in PDB entry 1EKF
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 ALA 161 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B GLU* 3.8 4.0 - - - +
43B TRP* 2.9 33.2 + - + +
48B TRP* 5.5 0.7 - - - -
109B LEU* 4.2 6.7 - - + -
110B PRO* 3.7 36.3 - - + -
146B LEU* 4.4 6.5 - - + -
147B ILE 3.3 14.1 - - - +
149B ASN* 4.0 7.3 + - - +
158B PRO* 5.4 0.2 - - + -
160B ARG* 1.3 79.3 - - - +
162B LEU* 1.3 63.9 + - - +
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B MET* 3.3 40.2 - - + -
41B VAL 3.4 13.7 - - - +
42B GLU* 3.4 30.5 - - + +
48B TRP* 5.5 0.2 - - - -
59B LEU* 4.0 9.6 - - + -
61B LEU* 5.6 3.8 - - + -
145B VAL 3.9 0.9 - - - +
146B LEU* 3.5 3.9 - - - -
147B ILE* 2.9 51.0 + - + +
149B ASN* 4.6 13.9 - - - +
161B ALA* 1.3 75.6 - - - +
163B LEU* 1.3 60.2 + - - +
164B PHE* 3.6 29.2 - - + -
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE* 4.4 14.6 - - + -
39B LEU* 4.7 1.1 - - + -
40B MET* 3.5 1.2 - - - +
41B VAL* 2.8 53.0 + - + +
48B TRP* 4.0 22.8 - - + -
100B MET* 4.1 22.0 - - + -
112B PHE* 4.2 17.7 - - + -
117B LEU* 4.2 21.3 - - + -
145B VAL 3.3 12.8 - - - +
146B LEU* 3.7 11.4 - - + -
162B LEU* 1.3 74.8 - - - +
164B PHE* 1.3 75.5 + - - +
165B VAL* 4.3 5.8 - - + -
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Residues in contact with PHE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PRO* 3.3 33.7 - - + -
68A LEU* 4.8 5.2 - - + -
69A HIS* 4.2 4.0 - + - -
38B MET* 4.2 16.4 - - + -
39B LEU 3.0 17.9 - - - +
40B MET* 4.1 13.7 - - + -
59B LEU* 3.8 20.6 - - + -
144B PRO 3.5 0.2 - - - -
145B VAL* 2.8 74.3 + - + +
147B ILE* 4.4 12.8 - - + -
162B LEU* 3.6 22.0 - - + -
163B LEU* 1.3 76.0 - - - +
165B VAL* 1.3 63.9 + - - +
166B ILE* 4.3 9.4 - - + -
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B MET* 3.3 10.2 - - - +
39B LEU* 3.0 55.1 + - + -
117B LEU* 4.7 0.7 - - + -
121B ILE* 4.2 14.4 - - + -
124B LEU* 3.8 15.2 - - + +
142B VAL* 3.7 29.8 - - + -
143B ARG 3.4 10.3 - - - +
144B PRO* 3.9 15.3 - - + -
163B LEU* 4.3 7.0 - - + -
164B PHE* 1.3 83.5 - - - +
166B ILE* 1.3 66.7 + - - +
167B LEU* 4.4 0.2 - - + -
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Residues in contact with ILE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PRO* 3.8 22.4 - - + +
64A ALA* 3.8 34.8 - - + +
69A HIS* 4.2 4.9 - - + -
153A LEU* 4.1 12.1 - - + +
34B PHE* 3.8 15.7 - - + -
37B HIS 5.0 0.4 - - - -
38B MET* 4.1 15.9 - - + +
56B PHE* 3.5 26.9 - - + -
143B ARG* 2.9 44.4 + - + +
164B PHE* 4.3 6.3 - - + -
165B VAL* 1.3 77.3 - - - +
167B LEU* 1.3 66.3 + - - +
168B CYS* 5.6 0.2 - - - -
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B PHE* 3.2 7.6 - - - +
35B THR* 3.0 53.8 + - + +
37B HIS 4.9 1.6 + - - +
56B PHE* 5.4 1.2 - - - -
124B LEU* 3.7 36.6 - - + -
125B ILE* 4.2 11.2 - - + -
128B ASP* 4.1 15.5 - - + +
140B LEU* 4.0 20.9 - - + -
141B TYR 3.4 2.2 - - - +
142B VAL* 3.8 36.1 - - + -
165B VAL* 4.4 0.2 - - + -
166B ILE* 1.3 87.1 - - - +
168B CYS* 1.3 63.7 + - - +
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Residues in contact with CYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 3.6 22.0 - - - -
31B GLY* 3.8 19.7 - - - +
33B THR 3.2 15.9 - - - +
34B PHE* 3.4 31.2 - - - -
140B LEU* 3.6 3.7 - - - +
141B TYR* 2.7 46.3 + - + +
166B ILE 5.6 0.2 - - - -
167B LEU* 1.3 72.9 - - - +
169B PRO* 1.3 71.2 - - - +
170B VAL* 3.4 3.2 + - + +
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Residues in contact with PRO 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B PRO* 4.7 9.6 - - + -
28B LEU* 4.0 22.2 - - + +
29B VAL 5.6 0.5 - - - +
30B PHE* 5.4 1.6 - - - -
31B GLY 5.4 2.8 + - - -
33B THR* 3.4 27.3 + - + +
35B THR* 4.2 12.3 - - + -
131B TRP* 3.7 45.8 - - + +
133B PRO* 3.9 10.3 - - + -
139B SER 3.7 5.6 - - - +
140B LEU* 3.9 5.6 - - + -
168B CYS* 1.3 87.3 - - - +
170B VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 4.2 4.4 - - - +
30B PHE* 3.7 40.8 - - + +
79B LYS* 5.0 11.9 - - - +
133B PRO* 4.1 3.6 - - - +
138B THR* 3.5 5.2 - - - -
139B SER* 2.7 39.1 + - - +
140B LEU 4.8 0.2 - - - -
141B TYR* 3.5 24.7 - - + +
168B CYS* 3.4 14.8 - - + +
169B PRO* 1.3 79.3 - - - +
171B GLY* 1.3 71.6 + - - +
172B ALA* 4.6 5.6 - - - +
173B TYR* 5.8 8.1 - - + -
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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