Contacts of the helix formed by residues 7 - 16 (chain C) in PDB entry 4PRO
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 7 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A ASN* 4.1 18.8 + - - +
84A SER* 4.2 20.9 - - - +
6C PRO* 1.3 79.3 - - + +
8C LEU* 1.3 62.1 + - - +
9C LYS 3.3 0.2 - - - -
10C PHE* 3.7 18.3 + - - +
11C ALA* 4.1 4.5 + - - +
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Residues in contact with LEU 8 (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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81A ASN* 4.3 4.8 - - - +
86A VAL* 3.6 28.0 - - + -
101A CYS* 3.7 15.5 - - - -
109A TYR* 2.8 42.8 - - + +
111A CYS* 4.2 1.8 - - - -
149A THR 4.4 1.1 - - - +
150A SER* 3.4 39.3 - - - +
6C PRO* 4.3 12.6 - - + -
7C GLN* 1.3 79.3 - - - +
9C LYS* 1.3 64.1 + - - +
10C PHE 3.1 0.9 - - - -
11C ALA* 3.1 13.3 + - - +
12C MET* 3.1 18.0 + - + +
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Residues in contact with LYS 9 (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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6C PRO* 3.1 34.3 + - - +
8C LEU* 1.3 80.0 - - - +
10C PHE* 1.3 60.2 + - - +
12C MET* 3.4 10.3 + - - +
13C GLN* 3.2 21.3 + - - +
18C ILE 4.8 1.2 - - - +
20C PRO* 5.4 14.1 - - + -
23C LEU* 3.7 32.3 - - + +
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Residues in contact with PHE 10 (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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6C PRO 4.1 1.7 + - - +
7C GLN* 3.7 13.9 + - - +
8C LEU 3.1 0.6 - - - -
9C LYS* 1.3 78.4 - - - +
11C ALA* 1.3 62.9 + - - +
13C GLN* 3.2 18.6 + - + +
14C ARG* 2.8 60.4 + - + +
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Residues in contact with ALA 11 (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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109A TYR* 4.0 15.3 - - + -
111A CYS* 3.5 26.2 - - - +
7C GLN 4.1 3.0 + - - +
8C LEU* 3.1 10.5 + - - +
10C PHE* 1.3 80.5 - - - +
12C MET* 1.3 57.7 + - - +
14C ARG* 3.8 27.1 - - - +
15C ASP* 2.9 34.7 + - - +
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Residues in contact with MET 12 (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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99A ALA* 4.1 25.1 - - + -
101A CYS* 4.8 10.3 - - - -
111A CYS* 5.0 2.0 - - - -
150A SER* 3.4 35.0 - - - +
8C LEU* 3.1 23.2 + - + +
9C LYS* 3.6 10.5 - - - +
11C ALA* 1.3 77.4 - - - +
13C GLN* 1.3 57.6 + - - +
16C LEU* 3.0 40.2 + - - +
17C GLY 3.2 2.9 + - - -
18C ILE* 3.3 23.5 + - + +
23C LEU* 4.0 27.1 - - + -
26C TYR* 4.4 10.1 - - + -
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Residues in contact with GLN 13 (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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9C LYS 3.2 10.5 + - - +
10C PHE* 3.7 20.2 - - + +
12C MET* 1.3 78.7 - - - +
14C ARG* 1.3 64.8 + - - +
17C GLY* 3.3 16.1 + - - -
18C ILE 3.2 17.2 + - - +
19C PHE* 3.8 35.9 - - + -
20C PRO* 3.7 23.8 - - + +
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Residues in contact with ARG 14 (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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109A TYR* 3.1 23.8 + - - -
110A GLN* 3.8 22.2 + - - +
10C PHE* 2.8 48.2 + - + +
11C ALA* 3.2 17.6 + - - +
13C GLN* 1.3 80.8 - - - +
15C ASP* 1.3 97.3 + - - +
17C GLY 4.7 0.7 + - - -
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Residues in contact with ASP 15 (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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110A GLN* 3.9 4.9 + - - -
111A CYS* 2.9 46.4 + - + +
112A GLY* 5.4 0.2 - - - -
177A ARG* 6.3 0.4 - - - +
11C ALA 2.9 15.2 + - - +
14C ARG* 1.3 118.7 + - - +
16C LEU* 1.3 67.6 + - - +
17C GLY 3.7 0.2 - - - -
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Residues in contact with LEU 16 (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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99A ALA* 3.5 26.2 - - + -
111A CYS* 4.4 7.4 - - + -
112A GLY* 3.4 37.0 - - - +
113A THR* 3.8 22.9 - - + +
135A ASN* 5.3 1.6 - - - +
12C MET* 3.0 23.4 + - - +
15C ASP* 1.3 84.8 - - - +
17C GLY* 1.3 61.0 + - - +
18C ILE* 3.0 14.5 + - + +
55C ARG* 2.8 23.4 + - - -
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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