Contacts of the strand formed by residues 161 - 170 (chain A) in PDB entry 1JEY
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 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLY 4.5 3.7 + - - -
35A ARG 3.3 10.1 - - - +
37A SER* 2.8 31.9 - - - +
82A LEU* 4.8 2.9 - - + -
108A LEU* 4.6 0.7 - - - -
154A PHE* 3.1 32.3 - - + +
157A VAL* 3.3 35.0 - - + +
159A PHE 3.9 0.4 + - - -
160A LYS* 1.3 81.7 - - - +
162A SER* 1.3 66.5 + - - +
163A HIS 4.9 0.7 - - - +
164A LYS* 3.2 41.9 + - + +
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Residues in contact with SER 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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34A GLY* 3.4 26.5 + - - -
35A ARG 3.2 5.4 + - - -
36A ASP* 3.0 16.9 + - - -
161A MET* 1.3 77.9 - - - +
163A HIS* 1.3 72.4 + - - +
164A LYS* 3.7 14.7 + - - +
34D C 5.1 3.5 + - - -
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Residues in contact with HIS 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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36A ASP* 3.2 12.8 + - - +
37A SER* 2.7 34.2 + - - -
161A MET* 4.9 0.2 - - - +
162A SER* 1.3 84.6 + - - +
164A LYS* 1.3 58.4 + - - +
165A ARG* 4.0 9.2 + - - -
199A PHE* 3.7 38.2 - + - -
252A ARG* 3.6 47.5 + - + +
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Residues in contact with LYS 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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154A PHE* 3.7 36.6 - - + -
161A MET* 3.2 38.0 + - + +
162A SER 3.7 15.9 + - - +
163A HIS* 1.3 77.4 + - - +
165A ARG* 1.3 60.3 + - - +
196A THR 5.6 3.7 + - - +
197A GLY 4.3 11.4 + - - +
198A ILE* 3.4 22.4 - - + +
199A PHE* 2.9 29.2 + - - -
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Residues in contact with ARG 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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37A SER 2.8 9.9 + - - +
38A LEU* 3.3 19.0 - - + +
39A ILE 2.9 25.5 + - - -
154A PHE* 3.5 5.2 - - - -
163A HIS* 4.7 8.9 + - + -
164A LYS* 1.3 75.0 - - - +
166A ILE* 1.3 68.3 + - - +
167A MET* 4.1 8.5 - - + -
199A PHE* 3.3 27.6 - - + +
201A ASP* 2.6 42.5 + - - +
249A LYS* 3.7 29.0 - - - +
252A ARG* 3.1 47.8 - - - +
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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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39A ILE* 3.5 10.8 - - + +
41A LEU* 4.1 29.8 - - + -
147A LEU* 4.4 6.3 - - + +
150A CYS* 3.6 29.8 - - + -
151A ALA 4.8 2.5 - - - +
154A PHE* 3.7 17.7 - - + -
165A ARG* 1.3 78.3 - - - +
167A MET* 1.3 60.3 + - - +
168A LEU 4.0 0.8 + - - +
193A LEU* 4.3 19.5 - - + -
198A ILE* 4.0 19.5 - - + -
199A PHE 2.7 12.2 + - - +
200A LEU* 3.3 12.5 - - + +
201A ASP* 2.7 34.1 + - - +
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Residues in contact with MET 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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38A LEU* 3.9 21.5 - - + -
39A ILE 2.9 13.9 + - - +
40A PHE* 4.3 13.2 - - + -
41A LEU 2.8 29.0 + - - +
165A ARG* 4.1 11.6 - - - -
166A ILE* 1.3 73.8 - - - +
168A LEU* 1.3 58.9 + - - +
169A PHE* 3.5 14.1 - - + -
201A ASP* 3.4 8.3 - - - +
203A MET* 3.5 37.5 - - + -
246A VAL* 3.9 29.6 - - - -
249A LYS* 3.9 33.7 - - + +
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Residues in contact with LEU 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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41A LEU* 3.5 22.9 - - + +
88A TYR* 3.5 37.7 - - + +
143A LEU* 5.0 7.4 - - + -
147A LEU* 6.2 0.7 - - + -
166A ILE* 4.0 1.5 + - + -
167A MET* 1.3 73.2 - - - +
169A PHE* 1.3 65.2 + - - +
170A THR* 4.1 7.9 - - + -
200A LEU* 4.7 17.9 - - + -
201A ASP 2.9 16.0 + - - +
202A LEU* 3.8 9.4 - - + +
203A MET* 2.7 32.8 + - - +
217A TYR* 3.4 42.4 - - + +
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Residues in contact with PHE 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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40A PHE* 3.9 33.2 - + + -
41A LEU 2.8 23.8 + - - +
42A VAL* 4.3 6.7 - - + -
43A ASP* 3.0 27.2 + - - +
48A MET* 3.6 5.1 - - + +
63A SER* 3.4 39.3 - - - +
66A CYS* 4.2 12.1 - - - -
67A ILE* 4.1 8.7 - - + -
167A MET* 3.5 30.3 - - + -
168A LEU* 1.3 73.8 - - - +
170A THR* 1.3 60.8 + - - +
203A MET* 3.6 14.8 - - + -
205A LEU* 4.2 2.0 - - + -
242A LEU* 4.2 10.3 - - + -
246A VAL* 4.0 24.5 - - + -
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Residues in contact with THR 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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43A ASP* 2.9 25.5 + - - -
48A MET* 3.7 9.4 - - - -
88A TYR* 3.8 7.6 + - - -
168A LEU* 4.1 5.2 - - + -
169A PHE* 1.3 76.0 - - - +
171A ASN* 1.3 60.6 + - - +
172A GLU* 3.0 27.0 + - - +
175A PRO* 6.1 0.2 - - - +
202A LEU* 3.9 24.2 - - + -
203A MET 3.6 4.4 + - - -
204A HIS* 3.3 5.2 - - - -
205A LEU* 2.9 24.4 + - - +
211A PHE* 3.7 4.0 - - + -
217A TYR* 4.1 13.1 + - + +
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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