Contacts of the helix formed by residues 12 - 18 (chain C) in PDB entry 1JXV
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 LYS 12 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C ALA 4.3 2.9 - - - +
11C ILE* 1.3 77.7 - - - +
13C PRO* 1.3 77.8 - - + +
14C ASP* 3.2 14.8 - - - +
15C GLY 2.9 11.4 + - - -
16C VAL* 3.2 9.5 + - - +
52C TYR* 3.8 22.7 + - - -
64C LEU* 5.6 4.0 - - - +
67C TYR* 4.9 5.8 - - + -
68C MET* 3.6 19.3 - - + -
72C PRO 4.3 1.1 - - - -
73C VAL* 4.1 2.5 - - - -
115C ASN* 2.8 34.4 + - - +
116C ILE 2.9 13.1 + - - +
117C ILE* 3.6 30.0 + - - +
118C HIS* 3.9 11.5 + - + +
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Residues in contact with PRO 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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149B TRP* 3.8 22.0 - - + -
12C LYS* 1.3 88.1 - - + +
14C ASP* 1.3 56.2 - - - +
16C VAL* 3.3 3.3 + - - +
17C GLN* 2.9 32.0 + - + +
67C TYR* 3.6 26.9 - - + +
68C MET* 3.9 13.0 - - - -
70C SER* 4.1 4.0 - - - +
71C GLY* 3.7 30.1 - - - +
72C PRO* 3.6 12.1 - - + +
73C VAL* 3.7 12.3 - - + -
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Residues in contact with ASP 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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149B TRP* 3.3 34.3 - - + +
12C LYS* 3.4 20.3 - - - +
13C PRO* 1.3 69.7 - - - +
15C GLY* 1.3 60.1 + - - +
17C GLN* 3.9 2.2 - - - +
18C ARG* 3.0 35.5 + - - +
67C TYR* 2.7 25.8 + - - +
114C ARG* 3.0 20.7 - - - +
115C ASN 4.6 0.2 + - - -
116C ILE* 2.9 34.5 + - + +
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Residues in contact with GLY 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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11C ILE* 3.8 16.8 - - - -
12C LYS 2.9 8.5 + - - -
14C ASP* 1.3 85.0 + - - +
16C VAL* 1.3 57.7 + - - +
18C ARG 3.9 0.3 - - - -
19C GLY 3.4 2.8 + - - -
20C LEU* 3.0 34.2 + - - +
21C VAL 4.2 0.7 + - - -
116C ILE* 3.6 23.3 + - - +
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Residues in contact with VAL 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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11C ILE* 4.2 6.3 - - + +
12C LYS 3.2 8.8 + - - +
13C PRO 3.7 5.8 - - - +
15C GLY* 1.3 73.9 - - - +
17C GLN* 1.3 66.1 + - + +
19C GLY* 2.9 15.2 + - - -
21C VAL* 4.1 13.9 - - + -
40C PHE* 4.1 13.9 - - + -
72C PRO* 3.6 25.8 - - + +
74C VAL* 4.0 26.0 - - + -
29E GLU* 4.3 2.6 - - - +
35E LEU* 5.6 2.7 - - + -
142E TYR* 3.7 30.5 - - + +
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Residues in contact with GLN 17 (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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149B TRP* 3.5 47.8 - - + -
13C PRO* 2.9 19.5 + - + +
14C ASP 3.9 4.5 - - - +
16C VAL* 1.3 76.8 - - + +
18C ARG* 1.3 60.1 + - - +
19C GLY 3.5 0.9 + - - -
72C PRO* 5.6 4.2 - - + +
142E TYR* 3.6 23.5 - - + +
143E THR 2.9 24.0 + - - -
144E SER* 3.5 8.5 + - - -
145E CYS* 2.7 45.0 + - - -
146E ALA* 5.7 0.7 - - - +
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Residues in contact with ARG 18 (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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29B GLU 5.2 1.0 + - - -
30B GLN* 3.7 14.1 + - - +
31B LYS 4.3 5.8 + - - -
32B GLY* 4.3 8.5 - - - -
146B ALA* 4.2 15.9 - - + -
149B TRP* 4.1 17.9 + - + -
150B ILE* 4.0 30.3 - - - +
14C ASP 3.0 18.1 + - - +
16C VAL 3.2 0.2 - - - -
17C GLN* 1.3 77.3 - - - +
19C GLY* 1.3 64.1 + - - +
20C LEU* 3.5 21.5 + - + +
108C PHE 2.5 29.4 + - - -
109C CYS* 3.4 11.7 - - - +
110C ILE 5.1 0.2 - - - +
114C ARG 5.1 0.4 + - - -
116C ILE* 3.1 26.6 - - - +
145E CYS* 5.4 1.3 - - - -
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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