Contacts of the helix formed by residues 87 - 98 (chain P) in PDB entry 6CNC
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 SER 87 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85P THR 3.8 1.0 + - - -
86P MET* 1.3 79.3 - - - +
88P ALA* 1.3 59.6 + - - +
89P GLU* 3.5 12.4 + - - +
90P GLU* 3.0 34.5 + - - +
91P ALA* 2.8 25.6 + - - +
124P CYS* 5.0 1.0 - - - +
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Residues in contact with ALA 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87P SER* 1.3 71.6 - - - +
89P GLU* 1.3 69.8 + - + +
91P ALA* 3.3 18.5 - - - +
92P LEU* 4.3 2.1 + - - +
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Residues in contact with GLU 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B PRO* 5.6 2.9 - - - +
87P SER* 3.5 10.5 - - - +
88P ALA* 1.3 81.9 - - - +
90P GLU* 1.3 62.2 + - - +
91P ALA 3.1 0.5 + - - -
92P LEU* 4.1 1.6 + - - +
93P VAL* 3.1 24.6 + - - +
116P LEU* 3.5 31.2 - - + +
120P VAL* 4.6 13.3 - - + +
123P LYS* 6.4 2.7 - - + -
124P CYS* 4.5 17.0 - - + -
383S ARG* 4.2 23.8 + - - -
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Residues in contact with GLU 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86P MET* 3.0 37.2 - - + +
87P SER* 3.0 22.1 + - - +
89P GLU* 1.3 74.8 - - - +
91P ALA* 1.3 59.8 + - - +
93P VAL* 3.6 9.0 - - - -
94P TYR* 2.4 39.4 + - + +
124P CYS* 2.9 40.6 - - + +
127P SER* 3.0 23.5 + - - -
128P LEU* 3.3 20.5 - - + +
131P GLN* 5.0 0.2 - - - +
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Residues in contact with ALA 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83P LYS* 5.0 10.2 - - - +
86P MET* 5.0 5.4 - - - +
87P SER 2.8 18.9 + - - +
88P ALA* 3.3 16.4 - - - +
89P GLU 3.1 1.8 - - - -
90P GLU* 1.3 77.9 - - - +
92P LEU* 1.3 62.4 + - - +
94P TYR* 4.4 1.3 - - - +
95P SER* 3.7 19.8 + - - -
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Residues in contact with LEU 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65P LYS* 5.7 10.8 - - + +
88P ALA 4.3 1.7 + - - +
89P GLU 4.1 2.9 + - - +
91P ALA* 1.3 77.5 - - - +
93P VAL* 1.3 66.7 + - + +
95P SER* 5.3 2.9 - - - -
96P TYR* 3.0 38.5 + - + +
113P ARG 5.6 5.8 - - - +
114P THR* 5.6 10.1 - - - +
362S ILE* 5.4 12.1 - - + -
379S MET 5.1 10.5 - - - +
380S VAL* 5.6 8.7 - - + -
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Residues in contact with VAL 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89P GLU 3.1 23.1 + - - +
90P GLU* 3.0 8.6 + - - +
92P LEU* 1.3 76.9 - - + +
94P TYR* 1.3 65.3 + - - +
96P TYR* 3.0 8.9 + - - +
97P ILE* 2.9 42.7 + - + +
110P ILE* 3.7 16.6 - - + -
114P THR* 3.8 27.4 - - + +
116P LEU* 4.8 7.9 - - + -
121P VAL* 5.6 3.1 - - + -
124P CYS* 4.6 17.5 - - - -
125P LEU* 5.3 2.5 - - + -
128P LEU* 5.0 4.0 - - + -
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Residues in contact with TYR 94 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79P GLU* 5.5 3.5 - - + +
82P LYS* 3.1 39.9 + - + +
83P LYS* 4.7 15.5 - - + -
86P MET* 4.3 12.6 - - + -
90P GLU* 2.4 40.2 + - + +
91P ALA 4.4 1.1 - - - +
93P VAL* 1.3 68.0 - - - +
95P SER* 1.3 64.6 + - - +
97P ILE* 2.7 41.4 + - + +
98P GLU* 3.2 23.8 + - - -
128P LEU* 3.8 24.7 - - + -
133P TYR* 3.5 34.5 - - + +
134P VAL* 5.6 2.0 - - + -
150P LEU* 4.1 18.9 - - + +
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Residues in contact with SER 95 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62P LYS* 3.6 25.2 + - - -
83P LYS* 4.2 9.5 - - - +
91P ALA 3.7 15.0 + - - -
92P LEU* 4.5 4.0 - - - -
93P VAL 3.5 0.6 - - - -
94P TYR* 1.3 85.0 - - - +
96P TYR* 1.3 59.8 + - - +
98P GLU* 3.2 36.5 + - - +
99P ALA* 3.6 6.4 + - - +
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Residues in contact with TYR 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65P LYS* 4.9 11.7 - - + -
92P LEU* 3.0 33.3 + - + +
93P VAL* 3.3 5.4 - - - +
95P SER* 1.3 75.1 - - - +
97P ILE* 1.3 64.9 + - - +
99P ALA* 3.2 25.4 - - + +
100P SER* 4.5 0.5 + - - -
105P ILE* 3.4 35.1 - - + +
109P THR* 4.3 0.7 + - - -
110P ILE* 4.2 21.1 - - + -
113P ARG* 2.5 73.0 + - + +
114P THR* 6.5 0.2 - - - -
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Residues in contact with ILE 97 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93P VAL* 2.9 36.3 + - + +
94P TYR* 2.7 23.1 + - + +
96P TYR* 1.3 69.2 - - - +
98P GLU* 1.3 58.2 + - - +
99P ALA 3.0 9.7 + - - -
100P SER* 3.2 20.1 + - - -
101P GLY 4.2 0.7 + - - -
105P ILE* 4.2 15.0 - - + +
110P ILE* 3.7 20.6 - - + -
125P LEU* 4.2 12.3 - - + -
128P LEU* 4.1 16.6 - - + -
134P VAL* 4.4 18.6 - - + -
148P TYR* 3.8 23.4 - - + +
149P MET* 5.0 5.7 - - - -
150P LEU* 5.4 2.7 - - + +
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Residues in contact with GLU 98 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62P LYS* 5.3 5.2 - - - -
79P GLU* 4.4 15.8 - - - +
83P LYS* 6.1 0.2 - - - +
94P TYR* 3.2 19.9 + - + +
95P SER* 3.2 37.4 + - - +
97P ILE* 1.3 75.9 - - - +
99P ALA* 1.3 66.1 + - - +
100P SER 3.2 0.4 - - - -
101P GLY* 3.2 17.4 + - - +
150P LEU* 3.5 43.7 - - + +
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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