Contacts of the strand formed by residues 101 - 110 (chain F) in PDB entry 7GCH
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 ASN 101 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91F ASN* 4.4 2.7 - - - +
93F LYS* 3.1 43.0 + - + +
94F TYR* 3.6 14.9 + - - +
99F ILE 3.8 0.2 + - - -
100F ASN* 1.3 93.1 + - - +
102F ASP* 1.3 56.3 - - - +
103F ILE* 3.2 11.8 + - - +
179G ALA* 2.8 31.4 + - - +
233G ALA 5.0 0.5 - - - +
234G LEU* 3.3 30.9 - - + +
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Residues in contact with ASP 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F THR 4.1 0.3 - - - +
55F ALA* 3.6 11.3 - - - +
56F ALA* 2.8 27.8 + - - -
57F HIS* 2.5 39.9 + - - -
94F TYR* 3.6 11.1 - - + -
99F ILE* 3.6 20.8 - - + +
101F ASN* 1.3 68.0 - - - +
103F ILE* 1.4 61.9 + - - +
179G ALA 5.5 0.2 + - - -
212G ILE* 4.2 2.8 - - - +
213G VAL 4.5 0.2 - - - +
214G SER* 2.9 29.7 + - - +
229G ALA* 3.5 22.1 - - + +
234G LEU* 4.5 2.0 - - - +
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Residues in contact with ILE 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F VAL* 4.0 17.5 - - + -
54F THR 3.3 7.2 - - - +
56F ALA* 3.6 11.4 - - - +
91F ASN* 3.2 36.7 + - + +
101F ASN 3.2 4.0 + - - +
102F ASP* 1.4 75.0 - - - +
104F THR* 1.3 65.0 + - - +
123F LEU* 6.5 0.7 - - + -
209G LEU* 5.8 0.7 - - + -
212G ILE* 3.1 29.2 - - + -
231G VAL* 5.0 7.4 - - + -
234G LEU* 3.5 35.4 - - + -
237G TRP* 3.7 18.8 - - + -
238G VAL* 4.2 16.2 - - + -
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Residues in contact with THR 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F VAL 3.8 0.3 - - - +
54F THR* 3.0 37.9 + - + +
55F ALA 3.8 15.0 - - - +
56F ALA* 3.7 6.0 + - - -
60F VAL* 4.9 4.5 - - + +
88F VAL* 4.4 12.6 - - + +
89F PHE 3.2 5.6 - - - +
90F LYS* 3.3 30.3 - - - +
103F ILE* 1.3 68.6 - - - +
105F LEU* 1.3 82.4 + - - +
106F LEU* 3.6 21.8 - - + -
237G TRP* 4.2 0.4 - - - -
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Residues in contact with LEU 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F ILE* 5.0 2.9 - - + -
51F TRP* 4.2 12.8 - - + -
52F VAL 3.3 4.0 - - - +
53F VAL* 2.7 41.1 - - + -
88F VAL* 3.8 0.5 - - - -
89F PHE* 2.8 42.7 + - + +
103F ILE* 4.6 0.7 - - + -
104F THR* 1.3 82.3 - - - +
106F LEU* 1.3 60.8 + - - +
237G TRP* 3.1 36.9 - - + -
238G VAL* 3.3 28.7 - - + -
241G THR* 4.4 6.1 - - - -
242G LEU* 4.3 15.0 - - + -
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Residues in contact with LEU 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LEU* 4.4 8.1 - - + -
51F TRP* 3.5 5.8 - - - -
52F VAL* 2.8 67.6 + - + +
54F THR* 4.1 13.0 - - + -
60F VAL* 3.6 28.5 - - + -
66F VAL* 3.8 20.0 - - + -
85F ILE* 4.2 17.9 - - + -
87F LYS 3.5 4.0 - - - +
88F VAL* 4.4 11.9 - - + -
104F THR* 3.6 23.3 - - + -
105F LEU* 1.3 75.6 - - - +
107F LYS* 1.3 62.9 + - - +
108F LEU* 3.8 1.7 + - + +
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Residues in contact with LYS 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F ASN* 3.6 22.9 + - - +
51F TRP* 3.5 41.7 - - + +
85F ILE* 3.7 2.6 - - - -
86F ALA* 2.7 32.3 + - + -
87F LYS* 3.0 21.2 + - + +
89F PHE* 4.0 10.1 - - + -
106F LEU* 1.3 73.2 - - - +
108F LEU* 1.3 73.8 + - - +
245G ASN* 4.0 18.4 - - - -
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Residues in contact with LEU 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F LEU* 4.8 4.5 - - + -
49F GLU 3.7 23.1 - - - +
50F ASN* 3.0 28.2 + - - +
51F TRP 4.2 2.2 - - - +
52F VAL* 4.3 13.9 - - + -
66F VAL* 3.5 41.3 - - + -
83F LEU* 3.9 21.8 - - + -
84F LYS 3.7 13.2 - - - +
85F ILE* 4.8 2.0 - - + -
86F ALA* 4.3 2.4 - - - +
106F LEU* 4.6 1.6 - - + +
107F LYS* 1.3 93.6 + - - +
109F SER* 1.3 64.1 + - - +
110F THR* 3.2 17.7 - - - +
112F ALA* 4.3 2.9 - - + +
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Residues in contact with SER 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F LYS* 3.2 36.9 + - - +
85F ILE 4.6 0.7 - - - -
86F ALA* 3.8 22.4 - - - -
107F LYS 3.8 1.4 + - - -
108F LEU* 1.3 74.2 - - - +
110F THR* 1.3 61.0 + - - +
111F ALA 4.3 0.2 - - - -
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Residues in contact with THR 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F LYS 5.0 2.0 - - - +
83F LEU* 3.0 41.6 - - + +
84F LYS* 4.3 11.2 - - + +
108F LEU* 3.7 12.9 - - - +
109F SER* 1.3 83.9 - - - +
111F ALA* 1.3 69.8 + - - +
112F ALA 3.4 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