Contacts of the strand formed by residues 161 - 170 (chain A) in PDB entry 1EKV
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A GLU* 4.0 2.9 - - - +
43A TRP* 2.8 46.6 + - + +
109A LEU* 3.8 8.7 - - + -
110A PRO* 3.8 24.2 - - + -
146A LEU* 4.4 3.1 - - + -
147A ILE 3.4 13.2 - - - +
149A ASN* 3.9 6.2 + - - +
158A PRO* 5.4 0.2 - - + -
160A ARG* 1.3 77.5 - - - +
162A LEU* 1.3 67.0 + - - +
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A MET* 3.7 29.8 - - - -
41A VAL 3.5 11.0 - - - +
42A GLU* 3.5 33.4 - - + -
43A TRP* 4.8 0.4 - - - +
48A TRP* 5.2 0.7 - - - -
59A LEU* 4.5 11.0 - - + -
61A LEU* 4.9 12.8 - - + -
145A VAL 3.9 0.3 - - - +
146A LEU* 3.1 6.4 - - - +
147A ILE* 2.9 49.8 + - + +
149A ASN* 4.8 11.0 - - - +
161A ALA* 1.3 81.2 - - - +
163A LEU* 1.3 60.2 + - - +
164A PHE* 4.3 16.4 + - + -
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PHE* 4.0 23.8 - - + -
39A LEU* 4.5 5.8 - - + -
40A MET* 3.5 0.9 - - - -
41A VAL* 2.9 38.0 + - + +
48A TRP* 4.1 14.1 - - + -
100A MET* 3.9 24.7 - - + -
112A PHE* 4.1 19.7 - - + -
117A LEU* 3.9 22.7 - - + -
145A VAL 3.2 13.0 - - - +
146A LEU* 3.7 9.9 - - + -
162A LEU* 1.3 76.1 - - - +
164A PHE* 1.3 75.2 - - - +
165A VAL* 4.3 7.0 - - + -
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Residues in contact with PHE 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A MET* 4.4 8.1 - - + -
39A LEU 3.2 15.5 - - - +
40A MET* 4.4 11.9 - - - -
59A LEU* 4.0 23.8 - - + -
143A ARG 3.8 0.2 - - - +
144A PRO 3.6 0.2 - - - -
145A VAL* 2.8 73.5 + - + +
147A ILE* 4.6 14.6 - - + -
162A LEU* 4.3 17.0 - - + -
163A LEU* 1.3 81.3 - - - +
165A VAL* 1.3 66.6 + - - +
166A ILE* 4.3 18.2 - - + -
63B PRO* 3.4 33.7 - - + -
68B LEU* 4.9 5.4 - - + -
69B HIS* 4.7 1.6 - - - -
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Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A MET* 3.2 12.1 - - - +
39A LEU* 3.1 55.1 + - + -
117A LEU* 4.9 0.4 - - + -
121A ILE* 4.2 15.5 - - + -
124A LEU* 4.0 15.5 - - + +
142A VAL* 4.0 11.9 - - + -
143A ARG 3.4 14.1 - - - +
144A PRO* 3.8 17.0 - - + -
163A LEU* 4.3 5.8 - - + -
164A PHE* 1.3 81.6 - - - +
166A ILE* 1.3 73.5 + - - +
167A LEU* 4.0 8.3 - - + -
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Residues in contact with ILE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A PHE* 3.6 25.4 - - + -
37A HIS 5.0 1.6 - - - -
38A MET* 4.1 12.6 - - + -
56A PHE* 3.3 32.1 - - + -
141A TYR 3.9 0.2 - - - +
143A ARG* 3.0 46.8 + - + +
164A PHE* 4.3 6.3 - - + -
165A VAL* 1.3 79.0 - - - +
167A LEU* 1.3 67.6 + - - +
168A CYS* 5.7 0.4 - - - -
63B PRO* 3.8 37.5 - - + +
64B ALA 4.3 0.2 - - - +
69B HIS* 4.2 2.0 - - + -
153B LEU* 4.1 17.0 - - + -
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A PHE* 3.3 9.0 - - - +
35A THR* 3.0 45.7 + - + +
37A HIS 4.8 2.1 + - - +
56A PHE* 5.3 1.2 - - - -
124A LEU* 3.8 40.6 - - + +
125A ILE* 4.1 19.3 - - + -
128A ASP* 4.4 8.1 - - + +
140A LEU* 3.8 24.7 - - + -
141A TYR 3.3 3.1 - - - -
142A VAL* 4.0 25.6 - - + -
165A VAL* 4.0 9.2 - - + -
166A ILE* 1.3 86.9 - - - +
168A CYS* 1.3 62.6 + - - +
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Residues in contact with CYS 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A PHE 4.1 10.1 - - - +
31A GLY* 4.1 13.7 - - - -
33A THR 2.5 25.1 - - - +
34A PHE* 3.9 11.7 - - + -
140A LEU* 3.3 4.5 - - - +
141A TYR* 2.7 44.7 + - - +
166A ILE 5.6 0.4 - - - -
167A LEU* 1.3 76.4 - - - +
169A PRO* 1.3 66.7 - - + +
170A VAL* 3.4 4.7 + - - +
153B LEU* 3.8 28.7 - - - -
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Residues in contact with PRO 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PRO* 4.7 3.4 - - + -
28A LEU* 3.6 32.1 - - + +
29A VAL 5.3 0.2 - - - +
30A PHE 3.8 7.8 - - - +
33A THR* 3.5 26.7 - - + +
35A THR* 4.4 10.8 - - + -
131A TRP* 3.5 22.4 - - + +
133A PRO* 3.5 21.5 - - + -
139A SER 3.4 6.5 - - - +
140A LEU* 3.4 8.7 - - + -
168A CYS* 1.3 85.8 - - - +
170A VAL* 1.3 61.1 + - - +
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Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 4.1 7.9 - - - -
30A PHE* 3.7 36.1 - - + +
79A LYS* 3.9 15.7 - - - +
133A PRO* 3.9 1.0 - - - +
138A THR* 3.3 5.6 - - - -
139A SER* 2.7 58.6 + - - +
140A LEU 4.4 0.2 - - - +
141A TYR* 3.7 17.0 - - + +
168A CYS 3.5 11.0 - - - +
169A PRO* 1.3 79.5 - - - +
171A GLY* 1.3 65.2 + - - +
173A TYR* 5.9 4.0 - - + -
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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