Contacts of the helix formed by residues 51 - 60 (chain Y) 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 ASP 51 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1384A C 3.9 0.2 - - - -
49Y ARG* 3.8 18.5 + - - +
50Y LEU* 1.3 73.4 - - - +
52Y PRO* 1.3 72.3 - - - +
53Y SER* 2.6 49.4 + - - +
54Y ILE* 2.7 21.5 + - - +
55Y ASN 3.7 0.7 + - - -
84Y ILE* 5.7 3.6 - - + -
85Y VAL 2.7 22.7 + - - +
86Y GLU* 3.8 12.3 - - + +
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Residues in contact with PRO 52 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1384A C 3.7 25.4 - - - +
1385A G 4.1 21.5 - - - +
1398A G 4.5 7.2 - - - +
1399A A 5.9 1.8 - - - +
49Y ARG* 4.3 8.7 - - - +
50Y LEU 3.4 5.1 - - - +
51Y ASP* 1.3 94.7 - - - +
53Y SER* 1.3 51.4 + - - +
54Y ILE 3.1 0.2 - - - -
55Y ASN* 2.9 9.0 + - + +
56Y GLU* 2.8 50.7 + - + +
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Residues in contact with SER 53 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Y ASP* 2.6 29.5 + - - -
52Y PRO* 1.3 74.9 - - - +
54Y ILE* 1.3 71.1 + - - -
56Y GLU* 3.4 9.2 + - - +
57Y ALA* 3.0 23.7 + - - +
86Y GLU* 3.6 3.4 - - - +
87Y ALA* 2.9 36.0 + - - +
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Residues in contact with ILE 54 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Y MET* 4.2 7.9 - - - -
33Y ILE* 3.8 32.5 - - + -
50Y LEU* 3.9 21.3 - - + -
51Y ASP 2.7 12.8 + - - +
53Y SER* 1.3 77.3 + - - +
55Y ASN* 1.3 62.2 + - - +
57Y ALA* 3.2 8.6 + - - +
58Y ALA* 3.1 19.9 + - - +
70Y ILE* 4.3 8.2 - - + +
72Y VAL* 3.3 27.1 - - + -
85Y VAL* 3.5 32.3 - - + +
86Y GLU* 3.6 19.1 - - - -
87Y ALA* 3.7 3.4 - - - +
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Residues in contact with ASN 55 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1383A U 2.5 45.4 + - - -
1384A C 3.2 34.9 + - - +
1399A A 4.2 6.9 + - - -
1400A C 3.9 13.7 + - - -
30Y MET* 3.1 19.8 - - + +
50Y LEU* 5.8 0.4 - - - +
51Y ASP 3.7 0.4 + - - -
52Y PRO* 2.9 12.9 + - + +
54Y ILE* 1.3 79.3 - - - +
56Y GLU* 1.3 66.3 + - - +
58Y ALA* 3.0 3.8 + - - -
59Y TRP* 3.0 35.3 + - - -
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Residues in contact with GLU 56 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1399A A 2.9 25.9 + - - +
1400A C 3.5 42.1 + - - +
52Y PRO* 2.8 35.7 + - + +
53Y SER* 3.8 6.9 + - - +
55Y ASN* 1.3 74.9 - - - +
57Y ALA* 1.3 57.9 + - - +
59Y TRP 3.6 0.5 - - - -
60Y ALA* 2.8 30.8 + - - +
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Residues in contact with ALA 57 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53Y SER 3.0 15.2 + - - +
54Y ILE* 3.3 11.0 - - - +
55Y ASN 3.1 0.2 - - - -
56Y GLU* 1.3 77.2 - - - +
58Y ALA* 1.3 62.0 + - - +
60Y ALA* 3.3 21.2 - - - +
61Y ARG* 5.3 0.7 + - - -
67Y PRO* 4.4 11.1 - - - +
70Y ILE* 3.8 20.4 - - + -
87Y ALA* 5.3 6.5 - - + -
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Residues in contact with ALA 58 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Y LEU* 5.9 1.8 - - + -
26Y ALA* 4.3 2.6 - - - +
29Y ALA* 4.8 15.0 - - + -
30Y MET* 3.1 35.9 - - + -
33Y ILE* 4.9 7.9 - - + -
54Y ILE 3.1 4.8 + - - +
55Y ASN 3.0 1.6 + - - +
57Y ALA* 1.3 80.1 - - - +
59Y TRP* 1.3 59.5 + - + +
60Y ALA 3.8 0.2 + - - -
61Y ARG 5.0 0.2 + - - -
62Y GLY 4.2 4.7 - - - +
65Y ASN 4.8 0.9 - - - +
66Y THR* 3.4 22.2 + - + +
67Y PRO* 4.2 14.2 - - + +
70Y ILE* 4.9 2.9 - - + +
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Residues in contact with TRP 59 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1381A A 3.5 20.2 - + - -
1382A G 3.4 45.8 - - - -
1383A U 3.1 29.2 + - - -
1400A C 3.7 17.5 - - - +
1401A G 3.3 30.0 - - - +
26Y ALA* 3.4 17.5 + - + +
27Y ASP* 3.5 21.1 - - - -
30Y MET* 3.4 15.2 - - + +
55Y ASN* 3.0 49.9 + - - +
56Y GLU 3.6 1.1 - - - -
58Y ALA* 1.3 77.0 - - - +
60Y ALA* 1.3 64.3 - - - +
61Y ARG 3.3 3.1 - - - -
62Y GLY* 2.9 19.2 + - - -
63Y ARG* 3.8 18.2 - - + -
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Residues in contact with ALA 60 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1400A C 5.5 1.1 - - - -
1401A G 4.6 11.8 + - - +
2743A A 4.8 5.5 + - - -
2744A G 5.8 0.2 - - - +
56Y GLU 2.8 11.8 + - - +
57Y ALA* 3.3 20.7 + - - +
58Y ALA 3.4 0.6 - - - -
59Y TRP* 1.3 77.6 - - - +
61Y ARG* 1.3 70.9 + - + +
62Y GLY 3.7 0.5 + - - -
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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