Contacts of the strand formed by residues 121 - 125 (chain B) in PDB entry 1JWL
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 GLY 121 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU 4.0 1.0 + - - -
64B ILE* 3.9 0.7 - - - +
65B GLY 3.0 24.1 + - - +
119B VAL* 3.3 4.3 - - - +
120B SER* 1.3 81.3 + - - +
122B LEU* 1.3 68.8 + - - +
143B VAL* 4.5 2.7 - - - +
144B PRO* 3.4 17.7 - - - -
304B LEU* 3.5 19.5 - - - +
308B SER* 5.8 0.2 - - - -
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLY* 3.4 3.1 - - - +
111B VAL* 3.2 40.2 - - + -
114B LEU* 3.4 29.2 - - + -
115B LEU* 3.9 9.9 - - + -
119B VAL* 3.4 30.7 - - + -
121B GLY* 1.3 76.6 - - - +
123B ILE* 1.3 62.0 + - - +
124B ILE* 4.1 17.3 - - + -
140B CYS* 3.8 13.2 - - - -
143B VAL* 4.9 2.5 - - + -
144B PRO 2.8 13.7 + - - +
145B ALA* 3.3 7.8 - - + -
146B LEU 2.9 23.9 + - - -
304B LEU* 3.3 8.2 - - - +
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Residues in contact with ILE 123 (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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64B ILE* 4.3 9.4 - - + -
65B GLY 2.9 10.6 + - - +
66B VAL* 3.4 9.8 - - + +
67B ALA 3.0 25.6 + - - +
83B ILE* 4.2 19.5 - - + -
122B LEU* 1.3 73.2 - - - +
124B ILE* 1.3 64.3 + - - +
125B ASN* 3.8 1.5 + - + +
146B LEU* 3.5 10.1 - - + +
148B LEU* 4.1 30.1 - - + -
300B SER* 3.6 38.8 - - - +
301B VAL* 4.2 6.7 - - + +
304B LEU* 3.6 25.6 - - + -
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Residues in contact with ILE 124 (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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67B ALA* 3.6 14.4 - - + +
107B CYS* 4.0 22.7 - - - -
111B VAL* 3.7 28.3 - - + -
122B LEU* 4.1 20.2 - - + -
123B ILE* 1.3 77.7 - - - +
125B ASN* 1.3 58.8 + - - +
126B TYR* 3.5 15.5 + - + +
128B LEU* 4.2 13.5 - - + -
136B VAL* 4.2 4.0 - - + -
140B CYS* 5.3 1.1 - - - -
145B ALA* 4.8 3.8 - - + -
146B LEU 2.8 11.4 + - - +
147B PHE* 3.7 29.5 - - + +
148B LEU 3.0 24.5 + - - -
149B ASP 4.0 1.2 + - - -
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Residues in contact with ASN 125 (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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66B VAL* 5.4 2.5 - - + -
67B ALA 2.7 14.3 + - - +
68B THR* 3.2 17.3 + - - +
69B SER* 3.0 28.0 + - - -
76B PRO* 4.0 13.3 - - - +
79B ILE* 3.6 29.7 - - + +
80B VAL* 5.9 0.2 - - - +
83B ILE* 6.3 0.7 - - + -
123B ILE* 3.8 4.1 + - + -
124B ILE* 1.3 69.2 - - - +
126B TYR* 1.3 59.3 + - - +
148B LEU* 4.2 24.8 - - + +
149B ASP* 4.2 14.3 + - - +
334B NPF 4.2 13.3 + - - -
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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