Contacts of the helix formed by residues 36 - 55 (chain A) 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 ASP 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ILE* 4.0 1.2 + - - +
35A GLY* 1.3 70.5 - - - -
37A THR* 1.3 60.0 + - - +
38A ARG* 2.7 44.1 + - - +
39A SER* 2.9 35.3 + - - -
40A ARG* 2.8 30.1 + - - +
195A LYS* 3.8 22.3 + - - +
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Residues in contact with THR 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLN* 5.8 1.8 - - - +
34A ILE* 4.1 16.8 - - + -
35A GLY 3.6 3.7 + - - +
36A ASP* 1.3 69.4 + - - +
38A ARG* 1.3 74.1 + - - +
39A SER 3.0 1.6 - - - -
40A ARG* 4.2 5.2 - - - -
41A THR* 2.7 39.7 + - - -
69A VAL* 3.7 28.5 - - + -
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Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASP* 2.7 33.1 + - - +
37A THR* 1.3 88.2 + - - +
39A SER* 1.3 56.9 + - - +
41A THR* 3.6 9.0 - - - +
42A ALA* 3.0 26.7 + - - +
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Residues in contact with SER 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ASP* 2.9 31.4 + - - -
37A THR 3.0 0.2 - - - -
38A ARG* 1.3 75.3 - - - +
40A ARG* 1.3 68.4 + - - +
41A THR 3.1 1.3 - - - -
42A ALA* 3.0 21.7 + - - +
43A GLU* 3.2 21.1 + - - +
195A LYS* 4.4 18.4 + - - +
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Residues in contact with ARG 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 3.9 17.0 - - + +
36A ASP 2.8 23.7 + - - +
37A THR* 3.8 10.1 - - - +
39A SER* 1.3 75.3 + - - +
41A THR* 1.3 63.0 + - - +
43A GLU* 3.5 11.1 + - - +
44A TYR* 2.8 48.4 + - - -
69A VAL* 3.8 15.5 - - + +
70A ASP* 3.0 15.8 + - - -
137A GLY* 4.8 1.0 - - - +
192A ILE 3.7 14.6 - - - +
193A TYR* 3.2 57.8 + - - +
194A TYR* 4.2 1.4 - - - -
195A LYS* 5.8 4.5 - - + +
293A SAM 2.6 42.6 + - - -
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Residues in contact with THR 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A THR* 2.7 25.3 + - - +
38A ARG* 3.6 11.0 - - - +
40A ARG* 1.3 77.0 - - - +
42A ALA* 1.3 55.3 + - - +
43A GLU 2.6 18.3 - - - +
44A TYR* 4.5 9.8 + - - -
45A LYS* 2.8 44.5 - - - +
69A VAL* 5.1 7.7 + - - +
70A ASP* 4.7 2.1 + - - -
73A MET* 3.3 28.1 - - - +
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ARG 3.0 21.4 + - - +
39A SER* 3.0 13.0 + - - +
41A THR* 1.3 79.7 - - - +
43A GLU* 1.3 68.6 + - - +
44A TYR 3.7 0.5 + - - -
45A LYS* 3.7 11.6 + - - +
46A ALA* 4.7 3.1 + - - +
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Residues in contact with GLU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A SER* 3.2 33.7 + - - +
40A ARG* 3.9 5.6 - - - +
41A THR 2.6 22.9 - - - +
42A ALA* 1.3 85.0 - - - +
44A TYR* 1.3 67.8 + - - +
45A LYS 2.7 5.9 + - - -
190A LYS* 6.2 2.2 - - - +
192A ILE* 3.4 40.4 - - + +
270A PHE* 5.5 0.2 - - + -
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Residues in contact with TYR 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ARG* 2.8 45.3 + - - +
41A THR* 4.5 5.5 + - - -
42A ALA 3.7 0.8 + - - -
43A GLU* 1.3 79.5 - - - +
45A LYS* 1.3 64.7 + - - +
46A ALA 3.4 2.0 - - - +
47A TRP* 3.8 12.1 - - - +
48A LEU* 3.0 39.4 + - + +
70A ASP* 2.6 29.7 + - - -
73A MET* 4.9 9.0 - - + -
136A LEU* 5.1 3.4 - - + -
192A ILE* 3.7 7.2 - - + -
193A TYR* 3.6 24.2 - + - -
270A PHE* 3.2 57.0 - + + +
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A THR* 2.8 35.7 - - + +
42A ALA* 3.7 7.3 + - - +
43A GLU 2.7 9.5 + - - -
44A TYR* 1.3 73.4 - - - +
46A ALA* 1.3 65.3 + - + +
49A LEU* 3.0 38.9 + - + +
73A MET* 3.3 35.5 - - + +
77A GLU* 2.9 30.5 + - - +
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Residues in contact with ALA 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA 4.7 3.6 + - - +
44A TYR* 4.5 0.2 - - - +
45A LYS* 1.3 82.7 - - + +
47A TRP* 1.3 57.6 + - - +
49A LEU* 4.1 4.5 - - - +
50A GLY* 3.1 22.9 + - - -
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Residues in contact with TRP 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TYR* 3.5 15.2 + - - +
45A LYS 3.2 0.6 - - - -
46A ALA* 1.3 78.0 - - - +
48A LEU* 1.3 105.0 + - + +
50A GLY* 3.2 0.9 + - - -
51A LEU* 2.8 51.1 + - + +
136A LEU* 5.6 0.2 - - + -
171A VAL* 4.0 7.6 - - + -
267A LEU* 3.4 36.5 - - + +
270A PHE* 3.7 39.9 - + + +
285A ILE* 4.0 12.8 - - + -
287A VAL* 3.5 20.9 - - + -
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TYR* 3.0 29.1 + - + +
45A LYS 4.1 1.6 - - - +
47A TRP* 1.3 101.4 - - + +
49A LEU* 1.3 58.9 + - - +
50A GLY 3.0 1.8 - - - -
51A LEU* 3.3 4.3 + - + -
52A LEU* 2.8 63.6 + - + +
70A ASP* 5.6 3.4 - - + +
73A MET* 4.5 11.9 - - + -
74A LEU* 5.0 5.2 - - + -
134A ILE* 4.8 9.6 - - + -
136A LEU* 3.9 25.1 - - + -
171A VAL* 4.3 20.2 - - + -
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A LYS* 3.0 35.6 + - + +
46A ALA* 4.3 4.5 - - - +
48A LEU* 1.3 77.0 - - - +
50A GLY* 1.3 61.0 + - - +
52A LEU* 4.1 4.2 - - - +
53A ARG* 3.1 54.6 + - - +
73A MET* 3.2 27.8 - - + -
74A LEU* 3.7 22.9 - - + -
77A GLU* 3.1 40.6 - - + +
79A PHE* 4.5 4.9 - - + -
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Residues in contact with GLY 50 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ALA 3.1 19.5 + - - -
47A TRP* 3.6 1.1 - - - -
48A LEU 3.0 0.6 - - - -
49A LEU* 1.3 76.5 - - - +
51A LEU* 1.3 52.8 - - - +
53A ARG* 2.8 8.9 + - - +
54A GLN* 2.5 40.6 + - - +
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Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A TRP* 2.8 58.5 + - + +
48A LEU* 3.9 4.5 - - + +
50A GLY* 1.3 71.2 - - - -
52A LEU* 1.3 62.7 + - + +
54A GLN* 4.0 11.4 - - - +
55A HIS* 3.0 59.4 + - + +
169A LEU* 3.6 18.0 - - + +
171A VAL* 4.3 9.9 - - + -
287A VAL* 4.0 23.1 - - + -
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 2.8 57.0 + - + +
49A LEU* 4.1 3.1 - - - +
51A LEU* 1.3 73.8 - - + +
53A ARG* 1.3 59.9 + - - +
56A GLY 3.4 0.9 + - - -
57A CYS* 2.9 40.4 + - + +
60A VAL* 4.3 14.6 - - + -
74A LEU* 3.8 31.4 - - + -
79A PHE* 3.8 19.3 - - + -
132A ALA* 3.7 29.6 - - + -
134A ILE* 5.0 5.4 - - + -
169A LEU* 5.2 4.9 - - + -
171A VAL* 5.6 3.1 - - + -
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Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 3.1 36.5 + - - +
50A GLY* 2.8 5.5 + - - +
52A LEU* 1.3 77.9 - - - +
54A GLN* 1.3 55.0 + - - +
55A HIS 2.9 5.2 - - - -
56A GLY* 2.5 26.5 + - - +
57A CYS 4.7 1.8 - - - +
77A GLU* 2.8 47.3 + - - +
79A PHE* 3.4 27.0 - - + -
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Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLY 2.5 21.7 + - - +
51A LEU* 3.5 9.5 + - - +
53A ARG* 1.3 71.6 - - - +
55A HIS* 1.3 80.6 + - + +
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Residues in contact with HIS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.0 46.4 + - + +
53A ARG 2.9 0.8 - - - -
54A GLN* 1.3 100.8 - - + +
56A GLY* 1.3 68.5 + - - +
57A CYS* 3.6 16.3 + - - -
165A ARG* 4.9 6.4 + - - -
167A GLY 5.5 1.8 - - - +
169A LEU* 4.0 19.3 - - + +
289A LYS* 3.5 32.0 - - - +
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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