Contacts of the helix formed by residues 45 - 52 (chain P) in PDB entry 1NJI
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 LEU 45 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P ASN* 1.3 68.4 - - - +
46P GLY* 1.3 66.8 + - - +
47P ARG 3.0 0.5 + - - -
48P ILE* 3.1 10.4 + - + +
49P GLU* 2.9 26.4 + - - +
64P VAL* 3.9 14.1 - - + -
65P LEU 3.2 9.1 + - - +
66P GLY* 4.1 6.3 - - - -
67P SER 3.0 11.8 + - - +
68P GLY 3.9 12.1 - - - +
69P VAL 4.5 0.4 - - - -
70P LEU* 4.3 20.8 - - + +
85P ALA* 4.7 4.0 - - + +
88P LYS* 3.3 47.1 - - + -
89P ILE* 3.6 33.0 - - + -
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Residues in contact with GLY 46 (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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700A A 3.7 17.0 + - - -
745A G 3.3 23.9 + - - -
44P ASN* 3.2 2.0 - - - +
45P LEU* 1.3 79.6 - - - +
47P ARG* 1.3 58.6 + - - +
49P GLU* 3.8 3.7 + - - +
50P ARG* 3.3 26.2 + - - +
67P SER 3.3 7.7 + - - -
68P GLY* 4.1 1.9 - - - -
69P VAL 4.5 9.6 - - - -
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Residues in contact with ARG 47 (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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701A U 4.8 5.3 + - - -
721A A 3.8 14.8 - - - -
722A G 3.5 20.8 + - - -
745A G 3.4 30.4 + - - -
746A A 4.8 5.1 + - - -
43P VAL* 3.6 19.2 - - + +
44P ASN 3.2 2.4 + - - +
45P LEU 3.1 1.0 - - - -
46P GLY* 1.3 74.4 - - - +
48P ILE* 1.3 69.1 + - - +
50P ARG* 3.0 35.9 + - - +
51P TYR* 3.2 27.2 + - + +
114P ILE* 4.0 4.6 - - + +
115P ARG 3.0 30.2 + - - -
8508P CL 3.6 24.8 - - + +
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Residues in contact with ILE 48 (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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43P VAL* 4.2 9.6 - - + -
44P ASN 3.9 10.5 - - - +
45P LEU* 3.1 13.2 + - + +
47P ARG* 1.3 76.4 - - - +
49P GLU* 1.3 64.4 + - - +
50P ARG 3.1 0.2 + - - -
52P ALA* 3.0 42.8 + - + +
58P VAL* 4.2 11.9 - - + -
60P VAL* 4.7 4.0 - - + -
64P VAL* 3.7 33.4 - - + -
70P LEU* 4.1 16.4 - - + -
74P VAL* 4.4 1.1 - - + -
76P VAL* 4.0 37.5 - - + -
89P ILE* 4.8 1.1 - - + -
114P ILE* 4.7 10.3 - - + -
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Residues in contact with GLU 49 (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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700A A 6.1 0.4 - - - +
115M ARG* 6.1 2.9 - - - +
45P LEU 2.9 11.7 + - - +
46P GLY 3.9 5.2 - - - +
48P ILE* 1.3 79.6 - - - +
50P ARG* 1.3 57.5 + - - +
69P VAL 3.2 24.2 - - - +
70P LEU* 3.5 10.5 - - + +
71P GLN* 2.6 42.2 + - - +
72P LYS* 3.0 49.4 + - - +
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Residues in contact with ARG 50 (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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700A A 3.1 38.0 + - - -
701A U 3.1 58.1 + - - +
744A G 3.8 6.3 + - - -
745A G 4.8 4.6 + - - -
46P GLY* 3.3 12.5 + - - +
47P ARG* 3.0 41.9 + - - +
49P GLU* 1.3 82.1 - - + +
51P TYR* 1.3 93.2 + - + +
52P ALA 3.7 0.2 - - - -
72P LYS* 4.5 5.8 + - - -
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Residues in contact with TYR 51 (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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701A U 4.1 18.4 + - - -
720A G 5.9 2.7 - - - -
721A A 3.6 54.5 - - - -
722A G 4.0 11.0 + - - -
47P ARG* 3.2 26.2 + - + +
48P ILE* 3.9 0.4 - - - -
50P ARG* 1.3 120.4 + - + +
52P ALA* 1.3 63.9 + - - +
53P GLN* 5.1 2.6 + - - -
56P GLU* 5.0 0.2 - - - +
72P LYS* 4.9 0.2 - - - -
112P ARG* 4.2 21.2 + - - +
114P ILE* 4.2 17.7 - - + -
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Residues in contact with ALA 52 (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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48P ILE* 3.0 24.4 + - + +
50P ARG 3.7 0.2 - - - -
51P TYR* 1.3 81.4 - - - +
53P GLN* 1.3 62.1 + - - +
56P GLU* 5.1 1.8 - - - -
58P VAL* 3.5 31.4 - - + -
72P LYS* 2.6 38.0 + - + +
74P VAL* 4.0 13.5 - - + -
112P ARG* 5.4 1.8 - - - -
114P ILE* 5.9 0.9 - - + -
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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