Contacts of the helix formed by residues 110 - 120 (chain P) in PDB entry 5C7O
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 110 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108P PHE 4.3 1.0 - - - +
109P ILE* 1.3 75.1 - - - +
111P PRO* 1.3 73.2 - - + +
112P GLU* 3.4 10.9 + - - +
113P TYR* 3.0 36.7 + - - +
114P MET* 2.8 27.5 + - - +
147P VAL* 4.7 0.2 - - - -
149P GLN* 3.4 14.7 + - - +
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Residues in contact with PRO 111 (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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110P ASP* 1.3 88.7 - - + +
112P GLU* 1.3 63.2 + - - +
114P MET* 3.2 11.3 + - + +
115P VAL* 3.1 24.3 + - - +
133P PHE* 4.0 21.3 - - + +
136P GLY* 3.9 28.9 - - - +
137P GLN 4.4 9.4 - - - +
138P LEU* 4.5 1.6 - - - +
147P VAL* 3.9 25.5 - - + +
149P GLN* 4.5 4.9 - - + +
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Residues in contact with GLU 112 (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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110P ASP* 3.3 8.3 + - - +
111P PRO* 1.3 79.2 - - - +
113P TYR* 1.3 62.3 + - - +
115P VAL* 3.4 17.0 + - - +
116P TYR* 3.5 6.6 + - - +
133P PHE* 3.4 47.6 - - + -
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Residues in contact with TYR 113 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108P PHE 4.1 16.4 - - - -
109P ILE* 3.6 17.0 - - + -
110P ASP* 3.0 26.7 + - - +
112P GLU* 1.3 74.1 - - - +
114P MET* 1.3 66.4 + - - +
116P TYR* 3.2 25.6 + + + +
117P MET* 3.0 54.9 + - + +
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Residues in contact with MET 114 (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 PHE* 3.8 20.2 - - + -
104P VAL* 3.5 37.2 - - + +
106P ASP* 4.1 17.9 - - + +
109P ILE* 3.4 31.0 - - + +
110P ASP 2.8 15.6 + - - +
111P PRO* 3.2 9.8 + - + +
113P TYR* 1.3 74.3 - - - +
115P VAL* 1.3 65.5 + - - +
117P MET* 3.8 1.1 - - - +
118P PHE* 2.9 28.1 + - - +
138P LEU* 4.3 15.3 - - + -
147P VAL* 3.6 37.0 - - + -
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Residues in contact with VAL 115 (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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111P PRO 3.1 15.0 + - - +
112P GLU* 3.4 10.1 - - + +
113P TYR 3.2 0.2 - - - -
114P MET* 1.3 76.8 - - - +
116P TYR* 1.3 56.9 + - - +
119P LYS* 2.9 47.4 + - - +
131P VAL* 3.7 32.2 - - + +
132P GLU* 3.4 33.7 - - - +
133P PHE* 3.7 12.1 - - + +
138P LEU* 3.6 9.9 - - + -
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Residues in contact with TYR 116 (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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112P GLU 3.5 7.0 + - - +
113P TYR* 3.2 35.7 + + + +
115P VAL* 1.3 81.3 - - - +
117P MET* 1.3 69.4 + - + +
119P LYS* 4.6 4.7 - - - +
120P TYR* 3.1 58.2 + + + +
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Residues in contact with MET 117 (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 PHE* 4.9 0.7 - - + -
88P ARG* 3.4 53.7 + - - +
109P ILE* 3.5 34.1 - - + -
113P TYR* 3.0 55.3 + - + +
114P MET* 4.0 4.0 - - - +
116P TYR* 1.3 82.3 - - + +
118P PHE* 1.3 58.0 + - - +
120P TYR 3.0 19.4 - - - +
121P ASP* 5.0 2.4 - - - +
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Residues in contact with PHE 118 (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 PHE* 3.9 14.8 - + + -
88P ARG* 3.5 33.4 - - + +
91P LEU* 3.5 31.9 - - + -
92P ARG* 3.1 38.7 + - + -
95P MET* 4.8 0.9 - - + -
114P MET 2.9 18.5 + - - +
115P VAL 3.9 2.0 - - - +
117P MET* 1.3 78.7 - - - +
119P LYS* 1.3 58.1 + - - +
127P TYR* 3.6 40.2 - + - +
131P VAL* 3.8 23.1 - - + -
138P LEU* 5.3 2.0 - - + -
140P VAL* 3.8 24.5 - - + -
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Residues in contact with LYS 119 (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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92P ARG* 3.9 0.2 + - - -
115P VAL* 2.9 29.9 + - - +
116P TYR* 3.4 4.0 + - - +
118P PHE* 1.3 78.9 - - - +
120P TYR* 1.3 91.6 + - + +
126P ARG* 3.2 11.2 - - + +
127P TYR* 2.9 38.0 + - + +
131P VAL* 3.2 42.8 + - + +
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Residues in contact with TYR 120 (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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88P ARG* 5.9 0.2 + - - -
92P ARG* 4.6 0.2 - - - -
116P TYR* 3.1 46.4 + + + +
117P MET* 3.0 21.0 - - - +
119P LYS* 1.3 107.5 - - + +
121P ASP* 1.3 60.5 + - - +
126P ARG* 3.7 49.7 + - + +
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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