Contacts of the helix formed by residues 83 - 102 (chain C) in PDB entry 4GCK
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 ASP 83 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C GLU* 2.9 15.6 + - - +
82C LYS* 1.3 78.1 - - - +
84C THR* 1.3 60.5 + - - +
85C THR* 3.3 12.9 + - - -
86C ALA* 2.9 29.0 + - + +
87C ARG* 2.9 31.9 + - - -
147C GLU* 3.7 14.7 - - - +
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Residues in contact with THR 84 (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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82C LYS 3.5 2.0 + - - -
83C ASP* 1.3 72.0 + - - +
85C THR* 1.3 67.7 + - - +
87C ARG* 3.1 12.5 + - - +
88C LEU* 3.0 44.3 + - + +
139C VAL* 3.8 20.3 + - + +
143C LYS* 3.6 31.4 + - + -
146C ARG* 4.2 13.5 - - - +
147C GLU* 3.6 19.1 + - - -
151C TYR* 4.0 13.2 - - + +
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Residues in contact with THR 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ASP* 3.3 11.4 + - - -
84C THR* 1.3 78.1 - - - +
86C ALA* 1.3 58.0 + - - +
88C LEU* 3.3 10.7 + - - +
89C ARG* 2.9 28.3 + - - +
143C LYS* 5.0 7.6 - - - -
147C GLU* 5.1 1.1 + - - -
151C TYR* 4.1 11.0 + - - -
190C TRP* 3.9 22.6 - - + +
194C ALA* 4.7 9.6 - - + -
197C LEU* 4.9 5.1 - - + +
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C GLU* 3.4 33.7 - - + +
83C ASP* 2.9 17.2 + - + +
84C THR 3.2 0.2 - - - -
85C THR* 1.3 77.4 - - - +
87C ARG* 1.3 57.6 + - - +
89C ARG* 3.3 10.5 + - - +
90C LEU* 2.9 35.7 + - + +
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Residues in contact with ARG 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ILE* 4.2 8.7 - - + +
78C LEU* 2.8 59.6 + - + +
81C GLU* 2.8 44.7 + - + +
82C LYS* 3.7 5.7 + - - +
83C ASP 2.9 23.6 + - - -
84C THR* 3.1 10.3 + - - +
86C ALA* 1.3 73.5 - - - +
88C LEU* 1.3 65.1 + - - +
90C LEU* 3.4 1.9 + - - +
91C ILE* 3.0 31.9 + - - +
139C VAL* 4.1 22.3 + - + +
142C GLU* 4.4 10.9 + - - +
146C ARG* 3.2 45.5 - - - +
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C THR* 3.0 40.1 + - + +
85C THR* 3.5 7.2 - - - +
87C ARG* 1.3 77.3 - - - +
89C ARG* 1.3 62.8 + - - +
91C ILE* 3.3 4.7 + - + +
92C VAL* 3.0 27.9 + - - +
136C LEU* 3.8 27.6 - - + +
139C VAL* 3.5 25.1 - - + -
140C MET* 4.2 19.1 - - + -
151C TYR* 3.6 16.4 - - - +
162C LEU* 3.9 13.9 - - + -
190C TRP* 3.8 13.9 - - + -
197C LEU* 4.0 7.6 - - + -
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Residues in contact with ARG 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C THR 2.9 16.8 + - - +
86C ALA* 3.5 11.8 + - - +
88C LEU* 1.3 77.0 - - - +
90C LEU* 1.3 81.1 + - - +
92C VAL* 3.4 0.9 + - - +
93C LEU* 2.9 36.5 + - - +
186C PHE* 3.7 19.0 - - + -
187C GLU* 2.6 35.8 + - - -
190C TRP* 3.4 50.0 - - + +
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Residues in contact with LEU 90 (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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77C ILE* 3.8 26.6 - - + +
80C ASP* 6.6 0.4 - - - -
81C GLU* 4.2 28.5 - - + +
86C ALA* 2.9 24.8 + - + +
87C ARG 3.9 2.7 - - - +
89C ARG* 1.3 92.6 - - - +
91C ILE* 1.3 61.9 + - - +
93C LEU* 3.7 15.2 - - + +
94C LEU* 2.8 30.7 + - - +
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Residues in contact with ILE 91 (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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74C ILE* 3.9 38.8 - - + -
77C ILE* 4.1 21.3 - - + -
78C LEU* 4.5 6.3 - - + -
87C ARG 3.0 25.6 + - - +
88C LEU* 3.8 4.3 - - + +
90C LEU* 1.3 74.2 - - - +
92C VAL* 1.3 66.6 + - + +
94C LEU* 3.3 2.9 + - - +
95C ILE* 3.0 38.3 + - + +
132C ILE* 5.0 0.9 - - + -
135C GLN* 5.7 2.5 - - + -
136C LEU* 3.9 30.5 - - + -
139C VAL* 4.5 19.1 - - + -
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Residues in contact with VAL 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LEU 3.0 19.7 + - - +
89C ARG 3.8 2.7 - - - +
91C ILE* 1.3 78.8 - - + +
93C LEU* 1.3 63.8 + - - +
95C ILE* 3.2 4.5 + - + +
96C LEU* 3.0 25.3 + - + +
136C LEU* 5.3 4.0 - - + -
162C LEU* 4.3 22.9 - - + -
165C PHE* 4.0 24.2 - - + -
166C CYS* 3.9 30.1 - - - -
186C PHE* 4.0 13.7 - - + -
190C TRP* 4.0 19.1 - - + -
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Residues in contact with LEU 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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89C ARG* 2.9 27.9 + - - +
90C LEU* 3.7 21.5 - - + +
92C VAL* 1.3 77.9 - - - +
94C LEU* 1.3 51.9 + - - +
96C LEU* 3.4 1.9 + - - +
97C GLY* 2.7 34.2 + - - -
183C THR* 4.2 18.8 - - + -
186C PHE* 3.7 44.2 - - + -
187C GLU* 5.6 0.2 - - - +
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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
----------------------------------------------------------
70C LEU* 3.8 18.6 - - + +
73C ARG* 3.5 58.8 - - + +
74C ILE* 3.7 29.2 - - + +
77C ILE* 4.2 10.1 - - + -
90C LEU 2.8 22.5 + - - +
91C ILE* 3.5 5.4 - - - +
93C LEU* 1.3 71.9 - - - +
95C ILE* 1.3 60.7 + - + +
97C GLY* 5.0 0.7 - - - -
98C PHE* 2.7 33.9 + - + +
101C ARG* 4.1 5.8 - - - +
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Residues in contact with ILE 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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70C LEU* 4.8 18.4 - - + -
74C ILE* 5.3 2.0 - - + -
91C ILE* 3.0 29.4 + - + +
92C VAL* 3.2 6.0 + - + +
94C LEU* 1.3 78.5 - - + +
96C LEU* 1.3 64.4 + - + +
98C PHE* 3.6 5.8 + - - +
99C GLY* 3.2 18.5 + - - -
109C LEU* 5.3 7.6 - - + +
129C PHE* 5.9 4.7 - - + -
132C ILE* 3.8 35.2 - - + -
136C LEU* 5.6 2.7 - - + -
163C LEU* 4.8 6.3 - - + -
166C CYS* 4.1 32.5 - - + -
170C LEU* 4.2 19.4 - - + +
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Residues in contact with LEU 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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92C VAL* 3.0 25.1 + - + +
93C LEU 3.9 2.5 - - - +
95C ILE* 1.3 77.4 - - + +
97C GLY* 1.3 60.0 + - - +
99C GLY* 3.3 1.2 + - - -
100C GLU* 2.9 29.8 + - - +
165C PHE* 4.0 24.7 - - + -
166C CYS* 3.9 41.3 - - + +
169C MET* 4.4 7.6 - - + -
170C LEU* 4.7 5.2 - - + -
182C PRO* 3.7 40.2 - - + +
183C THR* 3.9 8.7 - - + -
186C PHE* 4.1 17.5 - - + -
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Residues in contact with GLY 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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93C LEU* 2.7 22.3 + - - -
94C LEU* 3.8 0.7 - - - -
96C LEU* 1.3 69.3 - - - +
98C PHE* 1.3 66.1 + - - +
100C GLU* 3.3 3.5 + - - +
101C ARG* 2.9 38.9 + - - +
183C THR* 3.7 14.7 - - - +
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Residues in contact with PHE 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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65C PHE* 4.0 10.5 - + - -
66C ILE* 3.9 35.2 - - + -
69C SER* 3.6 24.7 - - - -
70C LEU* 3.7 26.5 - - + -
73C ARG* 4.8 3.8 - - - -
94C LEU* 2.7 23.0 + - + +
95C ILE 3.7 4.3 - - - +
97C GLY* 1.3 73.3 - - - +
99C GLY* 1.3 66.6 + - - +
101C ARG* 3.6 24.2 - - - +
102C ASN* 2.9 53.7 + - + +
105C LEU* 3.8 25.1 - - + -
106C THR* 5.7 0.7 - - - -
109C LEU* 5.1 7.6 - - + -
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Residues in contact with GLY 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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95C ILE 3.2 12.7 + - - -
96C LEU 3.8 2.5 - - - -
97C GLY 3.3 0.2 - - - -
98C PHE* 1.3 84.3 - - - +
100C GLU* 1.3 64.2 + - - +
102C ASN 3.1 16.1 + - - -
103C PRO 3.3 1.9 - - - -
106C THR* 2.9 29.7 + - - -
109C LEU* 5.8 2.0 - - - -
170C LEU* 4.2 9.9 - - - -
173C PHE* 3.4 8.1 - - - -
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Residues in contact with GLU 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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96C LEU 2.9 16.4 + - - +
97C GLY* 3.3 6.9 + - - +
99C GLY* 1.3 78.0 - - - +
101C ARG* 1.3 59.6 + - - +
102C ASN 3.5 0.2 + - - -
103C PRO* 3.7 13.7 - - - +
173C PHE* 3.7 13.2 - - + -
181C ARG* 3.3 36.8 + - - +
182C PRO* 3.2 13.4 - - + +
183C THR* 2.7 47.3 + - - -
184C ASP* 4.4 2.4 - - - +
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Residues in contact with ARG 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ARG* 2.6 41.5 - - - +
94C LEU* 4.1 10.9 + - - +
97C GLY* 2.9 23.7 + - - +
98C PHE* 3.6 34.3 - - - +
100C GLU* 1.3 76.8 - - + +
102C ASN* 1.3 72.1 + - - +
103C PRO* 3.4 7.6 - - - +
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Residues in contact with ASN 102 (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 PHE* 4.5 6.3 - - - -
98C PHE* 2.9 49.0 + - + +
99C GLY* 3.1 3.8 - - - -
101C ARG* 1.3 96.9 - - - +
103C PRO* 1.3 66.4 - - - +
104C GLY 3.3 1.8 - - - -
105C LEU* 3.1 34.2 + - + +
106C THR* 2.9 21.8 + - - -
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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
------------------------------------------------------------
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