Contacts of the helix formed by residues 44 - 55 (chain C) in PDB entry 1NBI
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 TYR 44 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C ARG* 2.7 42.4 + - - -
41C THR* 5.3 2.0 - - - -
43C GLU* 0.7 95.5 + - - +
45C LYS* 1.3 54.3 + - - +
46C ALA* 2.8 7.2 - - - +
47C TRP* 3.4 22.9 - + + +
48C LEU* 2.4 57.3 + - + +
70C ASP* 2.9 29.4 + - - -
73C MET* 4.7 5.6 - - + -
136C LEU* 5.4 3.1 - - + -
192C ILE* 3.4 10.1 - - + -
193C TYR* 3.1 27.1 - + - -
270C PHE* 3.1 47.6 - + + -
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Residues in contact with LYS 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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41C THR* 2.8 41.3 - - + +
42C ALA* 4.4 3.3 + - - +
43C GLU 2.6 3.0 + - - -
44C TYR* 1.3 78.9 - - - +
46C ALA* 1.3 58.2 + - + +
49C LEU* 2.9 38.5 + - + +
73C MET* 3.5 36.7 - - + +
77C GLU* 3.4 26.4 + - - -
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Residues in contact with ALA 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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42C ALA 4.9 6.0 + - - +
43C GLU* 5.8 3.1 - - - +
44C TYR* 4.7 1.8 - - - -
45C LYS* 1.3 79.9 - - + +
47C TRP* 1.3 56.6 + - - +
49C LEU* 3.7 2.6 - - - +
50C GLY* 2.8 34.0 + - - -
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Residues in contact with TRP 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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44C TYR* 3.4 20.7 - + + +
46C ALA* 1.3 78.3 - - - +
48C LEU* 1.3 108.0 + - + +
50C GLY* 2.9 4.7 + - - -
51C LEU* 2.9 41.7 + - + +
136C LEU* 4.9 5.2 - - + -
171C VAL* 3.4 15.7 - - + -
267C LEU* 3.7 26.3 - - + +
270C PHE* 3.2 52.2 + + + +
285C ILE* 3.2 35.4 - - + -
287C VAL* 4.8 0.2 - - + -
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Residues in contact with LEU 48 (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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44C TYR* 2.4 54.0 + - + +
45C LYS* 4.5 1.8 - - - +
47C TRP* 1.3 91.5 - - + +
49C LEU* 1.3 68.2 + - + +
51C LEU* 2.8 16.4 + - + -
52C LEU* 3.1 45.7 + - + +
70C ASP* 4.7 7.0 - - + +
73C MET* 5.3 2.0 - - + -
74C LEU* 4.5 12.3 - - + -
134C ILE* 4.5 19.1 - - + -
136C LEU* 4.2 20.2 - - + -
171C VAL* 5.0 3.4 - - + -
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Residues in contact with LEU 49 (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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45C LYS* 2.9 29.0 + - + +
46C ALA* 3.8 2.9 - - - +
48C LEU* 1.3 80.0 - - + +
50C GLY* 1.3 59.9 + - - +
52C LEU* 3.8 2.6 + - - +
53C ARG* 2.9 74.7 + - - +
73C MET* 3.1 32.5 - - - -
74C LEU* 4.0 9.6 - - + -
77C GLU* 3.8 14.4 - - + -
79C PHE* 3.3 32.1 - - + -
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Residues in contact with GLY 50 (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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46C ALA 2.8 15.8 + - - -
47C TRP* 2.9 4.2 + - - -
48C LEU 2.8 0.8 + - - -
49C LEU* 1.3 79.6 - - - +
51C LEU* 1.3 56.4 + - - +
53C ARG* 3.9 6.6 - - - +
54C GLN* 3.0 33.3 + - - +
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Residues in contact with LEU 51 (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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47C TRP* 2.9 40.5 + - + +
48C LEU* 2.8 15.6 + - + +
50C GLY* 1.3 70.3 - - - -
52C LEU* 1.3 64.0 + - + +
54C GLN* 3.5 9.5 + - - +
55C HIS* 2.9 56.8 + - + +
169C LEU* 3.7 13.1 - - + +
171C VAL* 4.3 12.8 - - + -
267C LEU* 5.6 0.4 - - + -
287C VAL* 3.6 31.0 - - + -
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Residues in contact with LEU 52 (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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48C LEU* 3.1 38.3 + - + +
49C LEU* 4.4 1.3 - - - +
51C LEU* 1.3 78.8 - - + +
53C ARG* 1.3 58.9 + - - +
55C HIS 3.1 3.5 + - - -
56C GLY 2.8 9.0 + - - -
57C CYS* 2.8 41.8 + - + -
60C VAL* 4.4 4.7 - - + -
74C LEU* 3.6 34.1 - - + -
79C PHE* 3.8 23.3 - - + -
132C ALA* 3.9 23.8 - - + -
134C ILE* 4.2 10.5 - - + -
169C LEU* 5.3 1.6 - - + -
171C VAL* 4.7 7.6 - - + -
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Residues in contact with ARG 53 (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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49C LEU* 2.9 62.2 + - - +
50C GLY* 3.9 6.9 - - - +
51C LEU 3.4 0.2 - - - -
52C LEU* 1.3 71.7 - - - +
54C GLN* 1.3 61.0 + - - +
55C HIS 3.0 1.8 - - - -
56C GLY* 2.6 24.8 + - - +
57C CYS 4.5 1.8 - - - +
77C GLU* 4.0 18.0 + - - +
79C PHE* 4.6 14.8 - - + -
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Residues in contact with GLN 54 (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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50C GLY 3.0 19.0 + - - +
51C LEU* 3.6 14.1 - - - +
52C LEU 3.3 0.2 - - - -
53C ARG* 1.3 76.0 - - - +
55C HIS* 1.3 75.5 + - + +
56C GLY 3.7 0.3 + - - -
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Residues in contact with HIS 55 (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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51C LEU* 2.9 44.5 + - + -
52C LEU 3.1 2.1 + - - +
53C ARG 3.0 0.4 - - - -
54C GLN* 1.3 93.6 - - + +
56C GLY* 1.3 66.0 + - - +
57C CYS* 3.6 19.9 - - - -
165C ARG* 4.9 9.4 + - - -
167C GLY 5.4 1.6 - - - +
168C GLY* 6.4 0.2 - - - -
169C LEU* 3.3 32.6 - - + +
287C VAL* 5.6 0.8 - - - +
289C LYS* 3.4 33.2 + - + +
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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