Contacts of the strand formed by residues 91 - 101 (chain C) in PDB entry 4G7Z
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 GLN 91 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C PRO* 3.3 9.7 - - - +
77C PRO* 2.9 31.0 - - + +
83C CYS* 5.4 0.2 - - - -
89C THR* 3.3 37.1 + - + +
90C TYR* 1.3 77.2 - - - +
92C ALA* 1.3 61.6 + - - +
117C HIS* 3.3 45.1 + - + +
118C ILE 3.4 20.6 - - - +
119C PRO* 3.8 5.5 - - + +
120C LEU* 3.6 8.3 - - - +
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C LEU* 5.0 10.2 - - + +
74C GLY 3.1 27.1 - - - +
75C GLU 4.4 3.1 - - - -
76C PRO* 4.9 0.4 - - + -
77C PRO* 4.5 0.2 - - - -
91C GLN* 1.3 75.5 - - - +
93C PRO* 1.3 72.5 - - + +
94C LEU* 3.4 1.2 + - - +
117C HIS* 4.1 4.9 - - - -
118C ILE* 3.1 29.5 + - - +
120C LEU* 3.5 22.8 - - + +
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Residues in contact with PRO 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ARG 3.9 0.5 - - - +
73C LEU* 3.7 4.2 - - - +
74C GLY* 3.0 35.1 + - - -
75C GLU 3.2 24.9 - - - +
77C PRO* 4.4 4.3 - - + -
92C ALA* 1.3 84.7 - - + +
94C LEU* 1.3 57.7 + - - +
95C TYR* 3.6 31.8 + - + +
114C PHE* 3.9 11.0 - - + -
116C GLY 3.6 9.0 - - - +
117C HIS* 3.7 19.2 - - + +
283F GLY 4.6 1.8 - - - +
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Residues in contact with LEU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ILE* 5.6 2.2 - - + -
48C PHE* 4.1 13.2 - - + -
71C TYR* 3.8 22.9 - - + -
72C ARG 3.2 18.6 - - - +
73C LEU* 3.6 18.2 - - + -
92C ALA 3.4 3.5 + - - +
93C PRO* 1.3 70.8 - - - +
95C TYR* 1.3 73.0 + - - +
96C ALA 4.8 0.2 - - - +
114C PHE* 4.2 0.8 - - - -
115C LEU* 3.0 52.7 + - + +
116C GLY 3.1 13.4 + - - +
118C ILE* 4.3 18.4 - - + -
344C PHE* 4.3 18.2 - - + -
378C LEU* 5.6 0.4 - - + -
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Residues in contact with TYR 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C TYR* 3.6 0.2 - - - -
72C ARG* 2.9 71.6 + - + +
74C GLY* 4.6 3.4 - - - -
93C PRO* 3.6 37.0 - - + +
94C LEU* 1.3 76.8 - - - +
96C ALA* 1.3 60.7 + - - +
112C GLU* 3.5 29.8 - - + +
113C VAL 3.4 9.0 - - - +
114C PHE* 3.3 35.7 - + + -
283F GLY* 4.4 14.5 + - - -
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Residues in contact with ALA 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C PHE* 4.1 19.5 - - + -
68C PHE* 4.7 4.3 - - + -
70C GLU 3.7 7.6 - - - +
71C TYR* 4.1 3.1 - - + +
94C LEU 4.2 0.4 + - - -
95C TYR* 1.3 75.3 - - - +
97C ARG* 1.3 58.9 + - - +
98C LEU* 3.9 8.9 - - + +
112C GLU* 4.1 2.2 - - - -
113C VAL* 2.9 41.2 + - + +
115C LEU* 3.8 27.1 - - + +
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Residues in contact with ARG 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C PHE* 4.1 0.2 - - - -
69C LEU* 2.9 43.9 + - - +
70C GLU* 2.8 56.2 + - + +
96C ALA* 1.3 69.9 - - - +
98C LEU* 1.3 66.2 + - - +
110C GLU* 3.2 34.4 + - + -
111C ASP 3.9 14.1 - - - +
112C GLU* 4.2 23.8 + - + +
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Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C PHE* 5.9 0.7 - - + -
52C PHE* 3.9 28.7 - - + -
66C LEU* 3.8 18.2 - - + -
67C ASP 3.3 5.2 - - - +
68C PHE* 3.7 28.0 - - + -
69C LEU* 4.9 1.8 - - - -
96C ALA* 3.5 9.4 + - + +
97C ARG* 1.3 83.3 - - - +
99C GLN* 1.3 61.0 + - - +
100C LEU 4.3 0.4 - - - -
110C GLU* 3.5 7.1 - - - +
111C ASP 3.1 30.3 + - - +
113C VAL* 3.5 28.7 - - + -
115C LEU* 6.2 2.0 - - + -
369C PRO* 4.0 5.0 - - + +
373C VAL* 4.1 20.6 - - + -
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Residues in contact with GLN 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C VAL 3.6 0.7 - - - +
66C LEU* 4.0 3.1 - - - -
67C ASP* 2.9 45.5 + - + +
69C LEU* 4.2 23.3 - - + +
98C LEU* 1.3 74.7 - - - +
100C LEU* 1.3 62.9 + - - +
101C ILE* 3.3 33.5 + - - +
108C ILE* 3.2 26.5 - - + +
109C LYS 3.8 4.9 - - - +
110C GLU* 3.8 22.7 - - + +
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C LEU* 3.6 19.7 - - + -
65C VAL 3.9 12.6 - - - +
66C LEU* 3.9 17.0 - - + +
99C GLN* 1.3 71.0 - - - +
101C ILE* 1.3 74.0 + - - +
107C LEU* 3.8 0.5 - - - +
108C ILE* 3.3 6.1 - - - -
109C LYS* 3.1 36.4 + - + +
359C MET* 4.8 1.3 - - - -
367C LEU* 3.2 48.0 - - + +
368C THR 4.0 2.7 - - - +
369C PRO* 4.1 6.4 - - + +
372C LEU* 3.6 24.2 - - + -
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Residues in contact with ILE 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C LEU* 3.3 11.5 - - - +
65C VAL* 2.7 58.2 + - + +
67C ASP* 4.5 9.4 - - + +
99C GLN* 3.3 33.0 - - - +
100C LEU* 1.3 76.5 - - - +
102C HIS* 1.3 74.1 + - - +
106C GLY* 4.6 5.2 - - - +
107C LEU 3.6 4.0 - - - +
108C ILE* 3.8 19.1 - - + -
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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