Contacts of the strand formed by residues 105 - 114 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83G VAL* 3.8 12.3 - - + -
97G TYR* 3.4 43.5 - - + +
98G LEU* 3.6 21.1 + - - +
100G ALA* 2.9 23.2 + - + +
101G GLU* 3.4 15.7 - - - +
102G LYS* 3.1 33.4 + - - +
103G GLU 3.4 1.4 - - - -
104G ASN* 1.3 77.1 - - - +
106G PHE* 1.3 60.4 + - - +
150G ALA* 2.8 33.1 + - - +
177G GLY 2.9 23.2 + - - -
178G ILE 2.8 21.5 + - - +
180G ASN* 2.9 33.1 + - - +
181G GLU 3.4 2.6 + - - -
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Residues in contact with PHE 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G LYS* 4.1 20.4 - - + -
83G VAL 2.8 16.0 + - - +
84G VAL* 4.0 5.2 - - + -
85G GLY 3.0 17.6 + - - -
97G TYR* 2.7 20.5 + - - -
103G GLU 3.9 14.1 - - - -
104G ASN* 3.4 29.4 - - - -
105G ARG* 1.3 72.5 - - - +
107G SER* 1.3 60.9 + - - +
179G VAL* 4.3 0.4 - - - -
181G GLU* 3.3 43.7 - - + +
183G ILE* 4.0 25.1 - - + -
188G GLY 3.8 14.4 - - - -
189G LEU* 3.6 29.4 - - + -
190G LYS* 4.9 5.4 - - - -
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Residues in contact with SER 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G VAL* 4.5 0.7 - - - -
85G GLY 3.6 7.4 + - - +
106G PHE* 1.3 74.5 - - - +
108G LEU* 1.3 82.3 + - - +
111G THR* 3.6 3.8 + - - -
113G TYR* 2.7 26.7 + - - -
170G VAL* 3.4 16.7 - - - +
179G VAL* 3.7 18.4 - - - -
181G GLU 3.0 6.8 + - - -
182G ILE* 3.4 3.7 - - - -
183G ILE* 2.8 31.0 + - - +
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Residues in contact with LEU 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F ASP* 3.5 31.6 - - + +
73F MET* 4.1 24.9 - - + +
76F PHE* 3.8 24.2 - - + -
56G PHE* 4.5 1.3 - - + -
84G VAL* 3.7 21.5 - - + +
85G GLY 2.9 12.9 + - - +
86G THR* 3.8 25.6 - - - +
107G SER* 1.3 81.9 + - - +
109G PRO* 1.3 69.1 - - + +
110G ASN 3.4 0.9 - - - -
111G THR* 2.8 20.4 + - - +
170G VAL* 3.9 1.2 - - - +
182G ILE* 4.7 0.2 - - - -
183G ILE* 3.6 17.3 - - + +
184G GLU* 5.3 0.9 - - - +
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Residues in contact with PRO 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F ASP* 3.4 17.5 - - - +
142F ARG* 5.5 2.1 - - - -
108G LEU* 1.3 86.7 - - + +
110G ASN* 1.3 64.8 + - - +
111G THR 3.1 5.9 + - - +
170G VAL* 3.4 23.4 - - + +
182G ILE* 4.2 16.4 - - + -
183G ILE 3.3 17.2 - - - +
184G GLU* 4.2 25.4 - - + +
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Residues in contact with ASN 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F ASP* 3.5 23.1 - - + +
71F HIS* 3.7 17.5 + - - -
72F ASP* 2.8 40.8 + - - +
142F ARG* 2.8 49.5 + - - +
146F LEU* 4.0 14.3 - - - +
87G GLY* 3.4 14.9 + - - +
109G PRO* 1.3 76.1 - - - +
111G THR* 1.3 61.2 + - - +
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Residues in contact with THR 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F ARG* 5.6 2.2 - - - +
85G GLY 3.4 1.2 + - - -
86G THR* 3.3 35.8 - - - +
87G GLY 3.2 14.6 - - - +
88G TRP* 4.1 2.7 - - - +
89G VAL* 4.3 2.5 - - + -
107G SER* 3.6 6.7 - - - -
108G LEU* 2.8 22.8 + - - +
109G PRO 3.1 4.1 + - - +
110G ASN* 1.3 76.5 + - - +
112G ARG* 1.3 67.6 + - - +
113G TYR* 3.5 23.3 - - + -
169G SER* 4.2 0.7 - - - -
170G VAL* 3.5 26.2 + - - +
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Residues in contact with ARG 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F VAL* 4.7 8.1 - - - +
65F GLU* 5.3 2.2 + - - +
120F GLY 5.5 0.8 + - - -
131F ILE* 3.8 14.6 - - - +
135F GLU* 3.3 43.3 + - - +
139F MET* 3.5 26.6 - - - +
142F ARG* 6.0 4.1 - - - +
87G GLY 3.1 12.2 + - - +
88G TRP* 3.3 40.9 - - + +
89G VAL 3.0 24.8 + - - +
111G THR* 1.3 73.6 - - - +
113G TYR* 1.3 65.2 + - - +
167G TRP* 3.7 32.2 - - + +
168G LEU 3.3 13.7 - - - +
169G SER* 4.9 2.7 - - - +
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Residues in contact with TYR 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85G GLY* 3.4 14.4 - - - -
89G VAL* 3.3 33.7 - - + -
94G ILE* 3.8 17.9 - - + -
97G TYR* 3.9 13.6 + + - -
107G SER* 2.7 32.7 + - - -
111G THR* 3.5 25.5 - - + +
112G ARG* 1.3 79.7 - - - +
114G MET* 1.3 61.5 + - - +
115G ILE* 5.8 0.2 - - - -
167G TRP* 3.5 3.2 - - - -
168G LEU* 2.6 45.4 + - + +
170G VAL* 4.5 4.7 - - + -
173G ALA* 3.6 25.4 - - + -
178G ILE* 4.0 11.9 - - + -
179G VAL* 3.5 21.2 - - + +
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Residues in contact with MET 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G GLN 5.8 0.2 - - - +
89G VAL 3.1 7.9 + - - -
90G ALA* 3.2 15.5 - - + -
91G SER* 3.0 33.3 + - - +
94G ILE* 3.3 3.7 - - - +
113G TYR* 1.3 75.4 - - - +
115G ILE* 1.3 63.3 + - - +
116G HIS* 3.6 25.2 + - + +
165G ASN* 4.0 22.2 - - - +
166G PHE* 3.4 30.3 - - + +
167G TRP* 3.7 45.7 - - + +
168G LEU* 5.5 0.9 - - - -
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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