Contacts of the strand formed by residues 39 - 47 (chain C) 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 ALA 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C VAL 3.1 4.9 + - - +
38C ILE* 1.3 76.5 - - - +
40C GLY* 1.3 57.7 + - - +
60C PHE* 3.6 8.6 - - - -
61C GLU* 2.9 48.0 + - + +
79C GLU* 3.9 22.7 - - - +
80C LEU 3.2 14.1 - - - +
81C GLN* 4.0 10.8 - - + +
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Residues in contact with GLY 40 (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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39C ALA* 1.3 75.7 - - - +
41C THR* 1.3 62.5 + - - -
58C VAL* 4.0 7.9 - - - -
59C GLU 3.0 15.9 - - - -
60C PHE* 3.7 11.4 - - - -
61C GLU* 4.3 1.6 - - - -
79C GLU* 3.4 8.7 - - - +
80C LEU 3.0 29.8 + - - -
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Residues in contact with THR 41 (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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40C GLY* 1.3 76.1 + - - -
42C VAL* 1.3 77.1 + - - +
43C VAL* 3.1 7.5 + - + +
58C VAL* 4.1 2.7 - - - -
59C GLU* 2.8 37.4 + - - -
77C GLY* 3.4 28.0 - - - +
78C ASP 3.4 2.6 + - - +
79C GLU* 4.9 6.4 + - - +
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Residues in contact with VAL 42 (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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41C THR* 1.3 76.1 - - - +
43C VAL* 1.3 60.6 + - - +
44C ASP 4.0 7.4 - - - +
45C ILE* 4.0 18.4 - - + -
56C ALA* 4.4 3.4 - - + -
57C ALA 3.5 11.0 - - - +
58C VAL* 4.3 5.4 - - + -
74C VAL* 3.6 25.1 - - + -
75C GLY 3.5 24.7 - - - +
76C VAL* 3.7 10.3 - - - +
77C GLY 2.9 23.9 + - - -
78C ASP* 2.9 20.2 + - + +
80C LEU* 3.9 22.2 - - + +
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Residues in contact with VAL 43 (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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41C THR* 3.7 15.7 - - + +
42C VAL* 1.3 73.9 - - - +
44C ASP* 1.3 61.1 + - + +
57C ALA 2.7 16.1 + - - +
59C GLU* 3.6 37.7 - - + +
65C ARG* 4.2 23.1 - - - +
76C VAL* 4.0 15.2 - - - +
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Residues in contact with ASP 44 (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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631 LYS* 3.0 30.6 + - - +
42C VAL* 3.6 3.7 - - - +
43C VAL* 1.3 86.2 - - + +
45C ILE* 1.3 89.1 + - - +
46C GLU* 4.4 11.1 - - + +
56C ALA* 3.6 0.2 - - - -
57C ALA* 2.7 44.3 + - + +
65C ARG* 5.1 2.9 - - - +
76C VAL* 4.2 8.4 - - - +
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Residues in contact with ILE 45 (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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541 ILE* 3.7 33.0 - - + +
631 LYS* 3.8 44.8 + - + +
641 ILE 4.6 7.2 - - - +
651 ALA* 5.1 5.6 - - + -
42C VAL* 4.0 11.4 - - + -
44C ASP* 1.3 96.5 + - - +
46C GLU* 1.3 64.7 + - - +
54C PRO* 4.2 11.9 - - + -
55C VAL 3.6 5.2 - - - +
56C ALA* 3.8 20.6 - - + +
70C ALA* 5.5 0.7 - - + -
74C VAL* 3.8 20.4 - - + +
76C VAL* 4.5 5.2 - - + -
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Residues in contact with GLU 46 (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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541 ILE* 3.8 6.3 - - - -
24C LYS* 3.1 30.1 + - - +
44C ASP* 4.4 16.6 - - - +
45C ILE* 1.3 81.3 - - - +
47C HIS* 1.3 60.7 + - - +
54C PRO* 3.2 4.9 - - - +
55C VAL* 2.5 53.5 + - + +
57C ALA* 4.0 9.0 - - - +
65C ARG* 4.6 6.2 + - - -
67C LEU* 3.7 25.1 - - + +
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Residues in contact with HIS 47 (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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521 THR* 4.3 10.5 + - - -
541 ILE* 3.9 12.9 - - + +
1653A A 3.2 32.7 + - - -
1654A U 3.0 89.2 + + + +
24C LYS* 2.4 35.4 + - - +
46C GLU* 1.3 73.8 - - - +
48C ASP* 1.3 65.4 + - - +
49C PRO* 3.3 6.6 - - - +
52C SER* 3.8 16.8 - - - -
53C ALA 4.2 5.2 + - - -
54C PRO* 4.5 1.1 - - - -
55C VAL* 5.3 0.4 - - - -
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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