Contacts of the strand formed by residues 107 - 112 (chain B) in PDB entry 1J3R
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 107 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B LYS* 1.3 76.7 + - - +
108B GLY* 1.3 58.7 + - - -
120B PHE* 4.8 1.3 - - - -
122B GLU* 3.7 5.5 - - - +
123B MET 2.8 28.4 + - - +
140B ILE 3.1 15.0 - - - -
142B THR* 3.4 19.8 + - - -
147B PHE* 3.5 10.6 - - - -
179B LYS* 5.5 1.4 + - - -
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Residues in contact with GLY 108 (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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107B GLY* 1.3 75.8 - - - -
109B MET* 1.3 59.8 + - - -
120B PHE* 3.6 20.0 - - - -
121B ILE 3.1 13.5 - - - -
122B GLU* 4.1 0.2 - - - -
123B MET* 2.9 17.4 - - - +
140B ILE* 2.8 32.5 + - - +
142B THR* 4.9 0.2 - - - +
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Residues in contact with MET 109 (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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100B TYR* 3.4 55.9 - - + -
108B GLY* 1.3 74.6 - - - -
110B LEU* 1.3 64.2 + - - +
111B LEU* 3.7 19.1 - - + +
119B ARG 3.7 1.2 - - - +
120B PHE* 3.3 6.3 - - - -
121B ILE* 2.8 34.7 + - + +
123B MET* 3.2 14.1 - - + +
129B VAL* 4.0 13.9 - - + -
131B VAL* 3.4 26.9 - - + -
137B HIS* 3.7 13.7 - - + -
138B ARG 3.3 12.8 - - - +
139B THR* 4.1 4.5 - - - +
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Residues in contact with LEU 110 (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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108B GLY 4.2 0.6 + - - -
109B MET* 1.3 73.2 - - - +
111B LEU* 1.3 65.0 + - - +
118B ALA* 5.0 1.1 - - + -
119B ARG 3.4 20.2 - - - +
120B PHE* 4.1 18.1 - - + -
137B HIS* 3.3 2.6 - - - -
138B ARG* 2.8 48.1 + - + +
140B ILE* 4.9 7.6 - - + +
169B PHE* 3.8 32.1 - - + -
171B LYS* 3.8 46.4 - - + +
172B ILE* 5.3 0.4 - - - -
173B VAL* 4.8 10.3 - - + -
181B VAL* 5.0 3.6 - - + -
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Residues in contact with LEU 111 (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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6A PRO* 3.7 24.2 - - + -
109B MET* 3.7 30.3 - - + +
110B LEU* 1.3 79.7 - - - +
112B GLN* 1.3 62.5 + - - +
118B ALA* 3.2 5.5 - - - +
119B ARG 2.7 40.4 + - - +
121B ILE* 4.0 24.5 - - + -
129B VAL* 5.2 0.4 - - + -
130B TYR 4.8 0.2 - - - +
131B VAL* 3.8 38.8 - - + -
135B TRP* 3.5 20.6 - - + -
136B ALA 3.2 8.5 - - - +
137B HIS* 4.2 2.0 - - + -
169B PHE* 4.5 1.3 - - - -
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Residues in contact with GLN 112 (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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90B TYR* 3.5 10.2 + - - +
111B LEU* 1.3 76.8 - - - +
113B THR* 1.3 70.6 + - - +
116B GLY* 4.3 8.7 - - - +
117B GLU 3.0 18.8 - - - +
118B ALA* 4.7 1.9 - - + +
135B TRP* 3.4 6.7 - - - -
136B ALA* 2.7 38.7 + - + -
164B ILE* 6.0 3.4 - - - +
168B GLY 4.1 2.8 + - - -
169B PHE* 3.2 26.1 - - + +
170B SER* 2.6 37.1 + - - +
187B LYS* 3.3 31.3 - - - +
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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