Contacts of the strand formed by residues 114 - 122 (chain B) in PDB entry 1J8H
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 LEU 114 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B PRO* 3.2 5.2 - - - +
104B ALA* 2.5 58.1 + - + +
113B ASN* 1.4 101.0 - - - +
115B LEU* 1.3 64.6 + - - +
116B VAL* 4.0 3.1 - - + -
160B MET* 3.7 39.0 - - + -
161B LEU 3.7 5.4 - - - +
162B GLU* 3.7 28.9 - - + +
163B THR 4.5 2.2 - - - -
165B PRO* 5.1 5.1 - - - +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B VAL* 3.5 31.0 - - + -
102B TYR 3.9 11.0 - - - +
103B PRO* 4.4 1.8 - - + -
114B LEU* 1.3 73.2 - - - +
116B VAL* 1.3 61.0 + - - +
131B TRP* 3.7 14.9 - - + -
160B MET* 3.3 2.9 - - - -
161B LEU* 2.8 42.5 + - + +
163B THR* 4.6 6.2 + - - +
165B PRO* 4.7 7.9 - - + -
171B TYR* 3.3 55.0 - - + -
188B TRP* 3.7 25.6 - - + -
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B THR 3.7 0.7 - - - +
101B VAL* 3.2 8.3 - - - +
102B TYR* 2.8 73.9 + - + +
104B ALA* 4.2 21.8 - - + -
114B LEU* 4.5 2.5 - - + -
115B LEU* 1.3 74.6 - - - +
117B CYS* 1.3 71.8 + - - +
118B SER 3.9 0.9 - - - +
131B TRP* 3.9 2.5 - - - -
158B LEU* 4.2 15.7 - - + -
159B VAL 4.1 2.2 - - - -
160B MET* 3.2 35.7 - - + -
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Residues in contact with CYS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 3.8 20.2 - - - -
100B THR 3.6 3.1 - - - -
101B VAL* 4.2 2.5 - - - -
116B VAL* 1.3 77.2 - - - +
118B SER* 1.3 58.3 + - - +
119B VAL* 3.8 13.0 + - - +
129B VAL* 4.2 0.9 - - - -
131B TRP* 3.5 15.9 - - + +
157B THR 3.8 0.3 - - - +
158B LEU* 3.5 1.2 - - - -
159B VAL* 3.0 37.0 + - + +
173B CYS* 2.0 50.0 - - + -
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Residues in contact with SER 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PRO* 3.9 19.8 - - - +
98B GLU 3.4 4.2 - - - +
99B VAL* 3.6 1.6 - - - +
100B THR 2.9 35.3 + - - -
102B TYR* 4.2 11.2 - - - -
116B VAL* 3.9 1.4 - - - +
117B CYS* 1.3 72.7 - - - +
119B VAL* 1.3 59.9 + - - +
120B ASN* 2.7 32.1 + - - -
157B THR 3.6 3.6 - - - -
158B LEU* 3.7 22.6 - - - +
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PRO* 3.7 16.6 - - + -
98B GLU 3.3 4.0 - - - +
99B VAL* 4.6 2.0 - - + -
117B CYS* 4.2 13.2 - - - +
118B SER* 1.3 74.4 - - - +
120B ASN* 1.3 62.7 + - - +
122B PHE* 3.3 25.4 - - + -
127B ILE* 3.6 15.0 - - + -
129B VAL* 4.0 10.1 - - + -
156B GLN* 3.1 5.4 - - - -
157B THR* 2.8 54.9 + - + +
175B VAL* 3.7 26.7 - - + -
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Residues in contact with ASN 120 (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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94A ASN 3.3 21.8 - - - +
95A SER* 4.1 7.6 - - - -
96A PRO* 3.3 21.4 - - - +
96B TYR 3.9 0.5 - - - +
97B PRO* 3.6 0.3 - - - +
98B GLU* 2.7 53.5 + - + +
100B THR* 5.4 1.0 + - - -
118B SER* 2.7 35.9 + - - -
119B VAL* 1.3 74.5 - - - +
121B GLY* 1.3 64.6 + - - +
122B PHE* 3.3 4.5 + - - -
155B PHE 3.9 2.5 - - - -
156B GLN* 3.3 26.7 + - - +
157B THR 4.8 0.2 + - - -
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Residues in contact with GLY 121 (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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94A ASN* 5.3 3.0 + - - +
95B VAL* 3.3 25.5 - - - +
96B TYR 3.5 4.8 - - - +
98B GLU* 5.5 3.6 - - - -
120B ASN* 1.3 74.7 - - - +
122B PHE* 1.3 60.0 + - - +
150B ASN* 4.9 2.3 + - - -
154B THR* 3.9 21.2 - - - +
155B PHE 3.1 12.1 + - - -
156B GLN* 4.8 0.6 - - - +
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Residues in contact with PHE 122 (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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95B VAL 3.3 12.6 - - - +
96B TYR 3.8 0.4 - - - -
97B PRO* 3.6 19.5 - - + -
119B VAL* 3.3 49.6 - - + -
120B ASN 3.3 1.5 - - - -
121B GLY* 1.3 77.6 - - - +
123B TYR* 1.3 61.5 + - - +
124B PRO 3.3 18.6 - - - -
125B GLY 3.6 22.0 - - - -
127B ILE* 3.6 22.4 - - + -
147B LEU* 3.7 21.8 - - + -
154B THR* 3.3 3.9 - - - -
155B PHE* 2.7 40.9 + - + -
156B GLN* 3.7 9.9 - - - -
157B THR* 4.1 6.1 - - + -
177B HIS* 3.5 11.2 - + - +
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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