Contacts of the strand formed by residues 105 - 114 (chain B) in PDB entry 4JCQ
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 ARG 105 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B VAL* 3.8 11.7 - - + -
97B TYR* 3.4 42.2 - - + +
98B LEU* 3.6 21.3 + - - +
100B ALA* 2.9 23.4 + - + +
101B GLU* 3.4 16.1 - - - +
102B LYS* 3.1 34.7 + - - +
103B GLU 3.5 1.4 + - - -
104B ASN* 1.3 77.0 - - - +
106B PHE* 1.3 60.0 + - - +
150B ALA* 2.8 32.7 + - - +
177B GLY 2.9 22.8 + - - -
178B ILE 2.8 21.1 + - - +
180B ASN* 2.9 33.1 + - - +
181B GLU 3.4 2.6 + - - -
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Residues in contact with PHE 106 (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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82B LYS* 4.1 19.7 - - + -
83B VAL 2.8 16.2 + - - +
84B VAL* 4.0 5.2 - - + -
85B GLY 3.0 17.6 + - - -
97B TYR* 2.7 20.0 + - - -
103B GLU 3.9 14.1 - - - -
104B ASN* 3.4 29.8 - - - -
105B ARG* 1.3 73.0 - - - +
107B SER* 1.3 61.0 + - - +
179B VAL* 4.3 0.4 - - - -
181B GLU* 3.3 44.4 - - + +
183B ILE* 4.0 24.5 - - + -
188B GLY 3.8 14.1 - - - -
189B LEU* 3.6 29.4 - - + -
190B LYS* 4.9 5.6 - - - -
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Residues in contact with SER 107 (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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84B VAL* 4.5 0.7 - - - -
85B GLY 3.5 7.9 + - - +
106B PHE* 1.3 74.1 - - - +
108B LEU* 1.3 82.5 + - - +
111B THR* 3.6 1.2 + - - -
113B TYR* 2.7 28.7 + - - -
170B VAL* 3.4 17.2 - - - +
179B VAL* 3.7 18.8 - - - -
181B GLU 3.0 7.2 + - - -
182B ILE* 3.4 3.0 - - - -
183B ILE* 2.8 28.0 + - - +
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Residues in contact with LEU 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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72A ASP* 3.4 34.3 - - + +
73A MET* 4.2 23.1 - - - +
76A PHE* 3.9 24.7 - - + -
56B PHE* 4.5 2.0 - - + -
84B VAL* 3.7 22.2 - - + +
85B GLY 2.9 12.5 + - - +
86B THR* 3.8 25.6 - - - +
107B SER* 1.3 81.1 + - - +
109B PRO* 1.4 67.2 - - + +
110B ASN 3.4 0.9 - - - -
111B THR* 2.8 20.5 + - - +
170B VAL* 3.9 1.4 - - - +
182B ILE* 4.7 0.2 - - - -
183B ILE* 3.6 17.7 - - + +
184B GLU* 5.3 1.6 - - - +
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Residues in contact with PRO 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP* 3.5 14.4 - - + +
142A ARG* 5.3 2.8 - - - -
108B LEU* 1.4 88.3 - - + +
110B ASN* 1.3 65.5 + - - +
111B THR 3.1 6.4 + - - +
170B VAL* 3.4 23.3 - - + +
182B ILE* 4.2 16.4 - - + -
183B ILE 3.3 17.9 - - - +
184B GLU* 4.2 24.5 - - + +
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Residues in contact with ASN 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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68A ASP* 3.5 22.2 - - + +
71A HIS* 3.7 18.3 + - - -
72A ASP* 2.9 39.2 + - - +
142A ARG* 2.8 49.6 + - - +
146A LEU* 3.9 14.2 - - - +
87B GLY* 3.3 15.5 + - - +
109B PRO* 1.3 76.1 - - - +
111B THR* 1.3 61.7 + - - +
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Residues in contact with THR 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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142A ARG* 5.5 3.3 - - - +
85B GLY 3.4 1.2 + - - -
86B THR* 3.3 35.5 - - - +
87B GLY 3.2 14.4 - - - +
88B TRP* 4.1 2.7 - - - +
89B VAL* 4.3 2.5 - - + -
107B SER* 3.6 7.2 - - - -
108B LEU* 2.8 22.7 + - - +
109B PRO 3.1 3.5 + - - +
110B ASN* 1.3 77.4 + - - +
112B ARG* 1.3 67.3 + - - +
113B TYR* 3.5 24.2 - - + +
169B SER* 4.6 0.7 - - - -
170B VAL* 3.5 26.3 + - - +
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Residues in contact with ARG 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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64A VAL* 4.7 8.1 - - - +
65A GLU* 5.2 1.8 + - - +
120A GLY 5.4 1.0 + - - -
131A ILE* 3.7 20.8 - - - +
135A GLU* 3.2 45.7 + - - +
139A MET* 3.4 27.6 - - - +
142A ARG* 5.9 4.7 - - - +
87B GLY 3.2 11.5 + - - +
88B TRP* 3.3 39.7 - - + +
89B VAL 3.0 24.9 + - - +
111B THR* 1.3 74.7 - - - +
113B TYR* 1.3 65.9 + - - +
167B TRP* 3.7 25.9 - - + +
168B LEU 3.4 12.8 - - - +
169B SER* 5.0 2.7 - - - -
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Residues in contact with TYR 113 (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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85B GLY* 3.4 14.9 - - - -
89B VAL* 3.3 34.1 - - + +
94B ILE* 3.8 17.0 - - + -
97B TYR* 3.9 13.3 + + - -
107B SER* 2.7 32.7 + - - -
111B THR* 3.5 25.1 - - + +
112B ARG* 1.3 78.5 - - - +
114B MET* 1.3 61.5 + - - +
167B TRP* 3.5 3.5 - - - -
168B LEU* 2.6 45.8 + - + +
170B VAL* 4.5 5.2 - - + -
173B ALA* 3.6 26.0 - - + -
178B ILE* 4.0 12.3 - - + -
179B VAL* 3.5 19.5 - - + +
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Residues in contact with MET 114 (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 GLN 5.8 0.4 - - - +
89B VAL 3.1 6.9 + - - -
90B ALA* 3.2 15.7 - - + -
91B SER* 3.0 33.1 + - - +
94B ILE* 3.3 4.0 - - - +
113B TYR* 1.3 76.2 - - - +
115B ILE* 1.3 63.3 + - - +
116B HIS* 3.6 25.3 + - + +
165B ASN* 4.0 22.0 - - - +
166B PHE* 3.4 30.1 - - + +
167B TRP* 3.7 45.3 - - + +
168B LEU* 5.5 1.6 - - - -
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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