Contacts of the strand formed by residues 129 - 135 (chain B) 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 LYS 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B LYS 3.5 2.4 + - - +
8B ALA* 3.2 17.5 - - + +
9B ALA* 2.7 31.2 + - - -
127B PHE* 3.2 4.0 - - - +
128B GLU* 1.3 99.5 - - + +
130B ARG* 1.3 64.1 + - - +
131B HIS* 5.8 0.7 - - + -
158B ASP* 5.6 1.6 - - - +
160B SER* 6.2 0.2 - - - +
239B LYS* 3.0 32.1 + - - +
240B ILE* 4.5 6.7 - - + -
243B HIS* 3.5 34.8 + - + -
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Residues in contact with ARG 130 (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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9B ALA* 3.2 14.1 - - + -
118B ILE* 3.7 34.1 - - + -
122B THR* 4.5 10.1 - - + -
127B PHE* 3.0 34.0 + - + +
128B GLU 4.0 10.9 + - - -
129B LYS* 1.3 76.3 - - - +
131B HIS* 1.3 60.2 - - - +
157B CYS* 2.9 22.9 + - - -
158B ASP* 2.9 44.5 + - - +
159B ILE* 3.5 9.6 - - + -
160B SER* 3.1 22.9 + - - -
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Residues in contact with HIS 131 (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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9B ALA 2.8 10.1 + - - +
10B VAL* 3.2 21.6 - - + +
11B VAL 2.9 23.9 + - - -
118B ILE* 3.9 3.4 - - - +
129B LYS* 5.5 0.7 - - + -
130B ARG* 1.3 75.3 - - - +
132B ILE* 1.3 69.3 + - - +
133B GLU* 3.4 30.2 - - + +
159B ILE* 4.4 0.2 - - - -
160B SER* 2.4 34.0 + - - +
161B LEU 3.7 15.3 - - - -
162B GLN* 2.6 42.1 + - + -
236B VAL 5.0 0.9 - - - -
239B LYS* 3.6 21.2 - - + +
240B ILE* 4.3 15.0 - - + -
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Residues in contact with ILE 132 (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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11B VAL* 3.4 14.8 - - + +
13B CYS* 4.6 1.1 - - + -
111B LEU* 3.9 13.0 - - + -
114B SER* 3.7 32.5 - - - +
115B MET* 3.7 31.0 - - + +
118B ILE* 3.6 15.7 - - + -
131B HIS* 1.3 83.7 - - - +
133B GLU* 1.3 64.9 + - - +
134B ILE* 4.0 11.2 - - + -
154B LEU* 4.9 0.2 - - + -
159B ILE* 4.0 10.3 - - + -
160B SER 3.1 6.4 + - - +
161B LEU* 3.4 25.2 - - + +
162B GLN 3.2 22.7 + - - -
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Residues in contact with GLU 133 (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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10B VAL* 4.8 1.4 - - + +
11B VAL 2.9 7.7 + - - -
12B LEU* 3.9 17.0 - - + +
13B CYS 2.7 32.4 + - - -
41B PHE* 4.0 9.3 - - - +
131B HIS* 3.4 32.1 - - + +
132B ILE* 1.3 71.6 - - - +
134B ILE* 1.3 58.0 + - - +
135B PHE* 3.3 30.2 - - + -
162B GLN* 3.5 13.3 - - + +
164B PHE* 3.6 13.2 - - + -
236B VAL* 2.6 41.8 - - - +
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Residues in contact with ILE 134 (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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13B CYS* 3.4 23.3 - - + +
59B PHE* 4.5 9.0 - - + -
107B PHE* 5.2 8.5 - - + +
111B LEU* 3.6 37.5 - - + -
132B ILE* 4.0 7.9 - - + -
133B GLU* 1.3 74.6 - - - +
135B PHE* 1.3 62.7 + - - +
136B THR* 4.0 24.0 + - + -
161B LEU* 4.3 3.4 - - + -
162B GLN 3.0 9.0 + - - +
163B PHE* 3.5 36.6 - - + +
164B PHE* 2.8 35.7 + - - +
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Residues in contact with PHE 135 (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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12B LEU* 3.9 11.7 - - + -
13B CYS 2.9 16.4 + - - +
14B MET* 3.7 5.1 - - + -
15B ASP* 2.8 32.0 + - - +
20B MET* 4.1 2.1 - - - +
34B ALA* 4.0 13.7 - - + -
37B VAL* 3.8 23.8 - - + -
38B ILE* 3.8 36.8 - - + -
41B PHE* 6.2 1.1 - - + -
59B PHE* 4.4 0.2 - - - -
133B GLU* 3.3 49.4 - - + -
134B ILE* 1.3 72.3 - - - +
136B THR* 1.3 59.2 + - - +
164B PHE* 3.4 34.3 - + + -
227B PHE* 4.0 19.3 - + + -
236B VAL* 5.3 0.2 - - + -
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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