Contacts of the strand formed by residues 56 - 61 (chain B) in PDB entry 5JES
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 SER 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ALA 4.0 1.8 + - - -
55B THR* 1.3 80.1 - - - +
57B LEU* 1.3 66.1 + - - +
68B VAL* 4.2 6.7 - - - -
69B GLU 3.4 9.9 - - - -
70B PHE* 3.5 23.4 - - - -
176B PHE 2.7 21.1 + - - -
177B THR* 3.5 13.7 - - - +
178B ASN* 3.2 5.2 + - - +
179B PHE* 2.9 38.7 + - - +
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Residues in contact with LEU 57 (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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55B THR* 4.1 14.8 - - + -
56B SER* 1.3 83.1 - - - +
58B ARG* 1.3 64.5 + - + +
69B GLU* 2.8 17.3 + - + +
70B PHE 4.2 3.4 - - - +
71B ASP* 3.8 37.0 - - + +
175B ASP* 3.8 6.9 - - - +
176B PHE 3.0 21.9 + - - -
177B THR* 3.9 13.7 - - + +
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Residues in contact with ARG 58 (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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57B LEU* 1.3 85.1 - - + +
59B ILE* 1.3 65.7 + - - +
60B LEU* 3.7 20.5 - - - +
68B VAL* 3.5 4.0 - - - +
69B GLU* 2.8 73.1 + - - +
173B SER* 3.5 27.6 + - - -
174B ALA 3.2 22.7 - - - +
175B ASP* 4.6 3.6 - - - +
176B PHE* 3.6 8.0 + - - +
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Residues in contact with ILE 59 (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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58B ARG* 1.3 75.7 - - - +
60B LEU* 1.3 62.6 + - - +
66B PHE* 3.7 26.2 - - + -
67B ASN 3.2 9.6 - - - +
68B VAL* 3.8 16.8 - - + -
160B VAL* 4.4 4.0 - - + -
163B VAL* 3.6 35.0 - - + -
164B LEU* 4.1 5.4 - - + -
167B ILE* 3.8 20.7 - - + +
173B SER* 3.1 5.4 - - - -
174B ALA* 2.9 52.9 + - + +
176B PHE* 4.0 15.9 - - + -
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ARG* 3.7 16.4 - - - +
59B ILE* 1.3 76.6 - - - +
61B ASN* 1.3 72.5 + - - +
62B ASN* 3.5 19.4 + - + +
66B PHE* 3.1 5.6 - - - -
67B ASN* 2.8 41.6 + - + +
69B GLU* 3.7 24.9 - - - +
167B ILE* 4.1 3.1 - - - -
171B GLY* 4.3 10.5 - - - +
172B LYS 3.5 18.4 - - - +
173B SER* 3.9 12.6 - - - -
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Residues in contact with ASN 61 (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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60B LEU* 1.3 73.0 - - - +
62B ASN* 1.3 57.0 + - - +
63B GLY* 2.8 18.5 + - - -
65B ALA 3.7 4.3 - - - -
66B PHE* 4.3 3.6 - - + +
167B ILE* 3.1 25.2 + - + +
168B LYS 3.0 27.1 + - - -
169B THR 3.3 17.0 - - - +
170B LYS* 3.5 1.9 - - - -
171B GLY* 2.8 33.4 + - - -
172B LYS 2.9 10.9 + - - +
229B LEU* 4.2 6.6 - - - +
230B ASN 3.1 12.7 + - - +
241B MET* 3.4 16.8 - - - +
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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