Contacts of the helix formed by residues 52 - 61 (chain B) in PDB entry 1N54
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 THR 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461A TYR* 6.5 1.1 - - + -
50B TYR 4.0 9.9 - - - +
51B THR* 1.3 75.1 - - - +
53B GLU* 1.3 64.8 + - - +
54B GLU* 2.8 24.4 + - - +
55B GLN* 2.9 42.3 + - + +
56B ILE* 3.3 17.8 + - - +
71B MET* 4.5 3.1 - - - -
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558A SER* 4.1 4.6 - - - -
559A PHE* 2.9 18.1 + - + +
560A SER* 2.6 48.0 + - - -
563A PHE* 5.4 1.7 - - - -
52B THR* 1.3 74.0 - - - +
54B GLU* 1.3 69.6 + - - +
55B GLN 3.1 0.5 + - - -
56B ILE* 3.1 6.9 + - - +
57B TYR* 3.0 44.1 + - + -
69B ILE* 3.8 24.8 + - + +
71B MET* 4.0 26.6 - - + +
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A ARG 5.8 0.2 - - - +
557A LYS 4.2 4.0 - - - +
558A SER* 3.3 14.8 - - - -
559A PHE* 3.1 64.6 + - + +
597A HIS* 4.8 7.9 - - + +
599A GLN* 2.7 38.7 + - - +
52B THR* 2.8 34.4 + - - +
53B GLU* 1.3 79.9 + - - +
55B GLN* 1.3 63.9 + - + +
57B TYR* 3.4 5.8 - - - +
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Residues in contact with GLN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A ARG 3.6 14.3 - - - +
459A LEU* 4.0 8.1 + - - +
460A SER* 3.0 45.8 + - - +
461A TYR* 4.5 5.5 - - - +
50B TYR 5.2 1.0 + - - -
51B THR* 3.3 8.8 - - + +
52B THR* 2.9 41.2 + - + +
53B GLU 3.2 0.8 - - - -
54B GLU* 1.3 76.1 - - + +
56B ILE* 1.3 68.0 + - - +
58B GLU* 3.0 14.4 + - - +
59B LEU* 3.3 11.4 + - - +
106B LEU* 4.7 9.8 - - + +
107B ASP* 2.9 30.7 + - - +
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Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL* 6.1 0.2 - - + -
47B LEU* 3.4 21.5 - - + -
51B THR* 4.1 11.7 - - + -
52B THR 3.3 9.8 + - - +
53B GLU 3.1 6.3 + - - +
55B GLN* 1.3 75.5 - - - +
57B TYR* 1.3 63.3 + - - +
59B LEU* 3.3 5.7 + - - -
60B PHE* 3.0 44.5 + - + +
69B ILE* 3.5 20.4 - - + -
71B MET* 4.2 16.6 - - - -
84B CYS* 3.3 28.7 - - - -
86B VAL* 4.1 13.0 - - + -
106B LEU* 4.1 11.4 - - + -
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Residues in contact with TYR 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A PHE* 4.2 9.0 - + + -
563A PHE* 3.3 33.7 - + - -
599A GLN* 4.0 4.7 - - - +
603A VAL* 4.1 14.6 - - + -
607A LYS* 4.7 0.3 + - - -
53B GLU* 3.0 37.6 + - + +
54B GLU* 3.4 13.0 - - - +
56B ILE* 1.3 77.9 - - - +
58B GLU* 1.3 62.8 + - - +
61B SER* 2.8 27.9 + - - -
66B ILE* 3.4 22.8 + - + +
67B LYS 3.6 19.2 + - - -
68B LYS* 4.2 6.8 - - - +
69B ILE* 3.3 40.0 + - + +
1555B GOL 3.5 22.2 - - - +
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Residues in contact with GLU 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A LYS* 3.3 36.6 - - - +
458A ARG* 2.9 39.0 + - + +
459A LEU* 3.4 23.2 - - + +
599A GLN* 3.5 10.8 + - - +
54B GLU 3.4 2.2 + - - -
55B GLN 3.0 9.6 + - - +
57B TYR* 1.3 79.2 - - - +
59B LEU* 1.3 64.0 + - - +
61B SER* 3.3 8.7 + - - -
62B LYS* 3.7 23.4 + - - +
1555B GOL 2.4 36.4 + - - -
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A HIS* 3.4 35.2 - - + +
459A LEU* 4.9 9.4 - - + -
55B GLN 3.3 7.2 + - - +
56B ILE 3.3 7.2 + - - +
58B GLU* 1.3 80.9 - - - +
60B PHE* 1.3 80.1 + - + +
61B SER 3.1 4.4 + - - -
62B LYS* 3.3 21.0 + - + +
101B ILE* 3.5 30.6 - - + +
104B THR* 4.7 5.2 - - - +
105B ARG 4.7 8.1 - - - +
106B LEU* 3.8 29.8 - - + -
111B ILE* 4.1 10.1 - - + -
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Residues in contact with PHE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LEU* 4.8 6.1 - - + -
44B VAL* 3.8 33.7 - - + -
56B ILE* 3.0 36.9 + - + +
59B LEU* 1.3 97.6 - - + +
61B SER* 1.3 57.0 + - - +
62B LYS 3.3 0.4 - - - -
63B SER* 3.8 4.6 + - - -
64B GLY 3.1 1.2 - - - +
66B ILE* 3.7 14.1 - - + +
86B VAL* 3.7 21.1 - - + -
88B TYR* 3.0 48.3 + + + +
97B ALA* 4.2 8.7 - - + -
101B ILE* 3.7 16.4 - - + -
106B LEU* 5.0 2.2 - - + -
111B ILE* 3.9 19.3 - - + -
113B THR* 4.2 10.3 - - + -
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Residues in contact with SER 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1558A GOL 4.7 8.3 + - - -
57B TYR* 2.8 20.5 + - - -
58B GLU 3.8 5.2 - - - -
59B LEU 3.1 1.8 - - - -
60B PHE* 1.3 76.6 - - - +
62B LYS* 1.3 61.8 + - - +
63B SER 3.0 5.8 - - - -
64B GLY* 3.1 21.9 + - - +
65B ASP* 5.1 2.5 - - - +
66B ILE* 2.9 18.6 + - - +
1555B GOL 3.1 27.4 + - - -
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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