Contacts of the helix formed by residues 41 - 54 (chain A) in PDB entry 3NBV
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 GLY 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.5 15.0 - - - -
13A VAL* 3.9 16.4 - - - +
40A GLY* 1.3 71.6 - - - -
42A ASN* 1.3 55.3 + - - -
43A ALA 3.6 1.6 - - - -
44A SER 3.3 0.2 + - - -
45A ASN* 2.7 35.9 + - - -
300A FRU 3.1 29.0 + - - -
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Residues in contact with ASN 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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41A GLY* 1.3 67.9 - - - -
43A ALA* 1.3 68.7 + - - +
44A SER 3.1 0.2 + - - -
45A ASN* 3.2 3.1 + - - +
46A SER* 2.9 28.0 + - - -
139A GLU* 3.6 23.9 + - + +
171A GLU* 2.8 32.2 + - - +
173A GLU* 3.3 30.2 + - - +
174A LYS* 5.0 1.4 - - - +
258A ASP* 3.3 21.0 + - - +
300A FRU 2.8 36.2 + - - +
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Residues in contact with ALA 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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8A CYS* 3.7 15.3 - - + +
9A VAL 3.7 7.4 - - - +
10A GLY* 3.5 40.2 - - - +
11A LEU 4.0 0.2 + - - -
42A ASN* 1.3 79.0 - - - +
44A SER* 1.3 61.3 + - - +
46A SER* 3.4 6.6 + - - -
47A CYS* 3.2 27.0 + - - -
59A PHE* 4.1 7.6 - - + -
137A HIS* 5.5 4.5 - - + -
139A GLU* 3.2 9.7 + - + +
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Residues in contact with SER 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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11A LEU 3.6 10.7 + - - -
12A VAL* 3.7 12.3 - - - -
39A ARG* 2.5 51.9 + - - +
40A GLY 3.0 28.8 + - - -
41A GLY 3.3 0.8 + - - -
42A ASN 3.1 0.4 - - - -
43A ALA* 1.3 76.9 - - - +
45A ASN* 1.3 64.0 + - - +
47A CYS* 3.2 11.5 + - - +
48A THR 3.2 5.0 + - - -
59A PHE* 4.1 8.3 - - - -
76A PHE* 4.1 4.3 - - - -
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Residues in contact with ASN 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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15A ASP* 4.9 0.2 + - - -
38A GLN* 5.3 0.2 - - - +
39A ARG 3.3 21.1 - - - +
40A GLY* 3.6 2.1 - - - -
41A GLY 2.7 17.3 + - - +
44A SER* 1.3 72.4 + - - +
46A SER* 1.3 62.0 + - - +
48A THR* 3.2 9.6 + - - -
49A VAL* 3.1 27.0 + - - +
254A LEU* 5.7 1.4 - - - +
255A GLY* 4.3 4.0 - - - +
258A ASP* 3.0 35.4 + - + +
294A PHE* 3.3 30.9 - - + -
300A FRU 3.2 29.7 + - - -
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Residues in contact with SER 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A CYS* 4.3 13.7 - - - -
42A ASN 2.9 20.4 + - - -
43A ALA* 3.6 8.0 - - - -
45A ASN* 1.3 76.4 - - - +
47A CYS* 1.3 57.6 + - - +
49A VAL* 3.1 3.3 + - - +
50A LEU* 2.8 34.8 + - - +
137A HIS* 5.1 8.7 + - - -
258A ASP* 3.5 19.7 + - - +
261A ASN* 4.6 5.5 + - - +
262A ALA* 3.6 20.0 + - - +
265A ILE* 5.9 1.3 - - - -
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Residues in contact with CYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A CYS* 3.8 15.3 - - - -
43A ALA 3.2 19.1 + - - -
44A SER* 3.2 8.9 + - - +
46A SER* 1.3 73.3 - - - +
48A THR* 1.3 66.9 + - - +
50A LEU* 4.3 2.0 - - - -
51A SER* 2.8 26.9 + - - -
57A CYS* 3.6 18.6 - - - -
58A ALA 3.7 24.9 - - - -
59A PHE* 3.8 18.2 - - - -
76A PHE* 4.7 3.6 - - + -
81A VAL* 4.0 17.0 - - + +
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Residues in contact with THR 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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39A ARG* 2.7 35.3 + - - +
44A SER 3.2 3.8 + - - -
45A ASN* 3.3 15.4 + - - -
47A CYS* 1.3 78.8 - - - +
49A VAL* 1.3 59.6 + - - +
51A SER* 3.4 5.5 + - - -
52A LEU* 3.0 35.1 + - + +
79A ARG* 3.8 26.9 - - - +
294A PHE* 3.9 36.5 - - + -
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Residues in contact with VAL 49 (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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45A ASN 3.2 16.2 - - - +
46A SER 3.1 1.2 + - - +
48A THR* 1.3 75.0 - - - +
50A LEU* 1.3 66.6 + - - +
52A LEU* 3.1 8.8 + - - +
53A LEU* 2.9 40.8 + - + +
259A THR* 3.8 40.4 - - + +
262A ALA* 3.5 24.2 - - + -
263A SER* 4.1 3.4 - - - +
284A VAL* 4.7 0.4 - - + -
294A PHE* 4.1 15.9 - - + -
297A ILE* 4.1 17.0 - - + -
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Residues in contact with LEU 50 (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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6A ILE* 4.0 34.3 - - + -
8A CYS* 3.9 26.7 - - - -
46A SER* 2.8 24.1 + - - +
47A CYS* 3.7 3.8 - - - +
49A VAL* 1.3 71.7 - - - +
51A SER* 1.3 62.6 + - - +
53A LEU* 3.0 15.4 + - + +
54A GLY 3.0 0.2 + - - -
55A ALA* 3.0 27.0 + - + +
57A CYS* 3.9 20.0 - - + -
262A ALA* 3.6 29.6 - - + +
265A ILE* 4.6 4.9 - - + -
266A PHE* 4.0 17.7 - - + +
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Residues in contact with SER 51 (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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47A CYS 2.8 20.6 + - - -
48A THR 3.5 5.7 + - - -
50A LEU* 1.3 72.8 - - - +
52A LEU* 1.3 65.1 + - - +
54A GLY* 3.0 14.4 + - - -
55A ALA 4.0 9.4 + - - -
57A CYS* 4.2 3.1 - - - -
79A ARG* 2.7 43.6 + - - +
80A GLY 5.6 0.4 - - - -
81A VAL* 4.5 4.9 - - - -
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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 THR* 3.0 23.4 + - + +
49A VAL* 3.1 6.5 + - - +
51A SER* 1.3 80.0 + - - +
53A LEU* 1.3 59.5 + - + +
54A GLY* 3.2 1.1 + - - -
79A ARG* 3.6 28.0 - - - +
294A PHE* 3.4 40.4 - - + +
295A ASP* 4.6 4.7 - - - +
297A ILE* 3.8 18.4 - - + -
298A VAL* 3.6 39.8 - - + +
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Residues in contact with LEU 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 VAL* 2.9 28.7 + - + +
50A LEU* 3.0 10.2 + - - +
52A LEU* 1.3 79.1 - - + +
54A GLY* 1.3 57.1 + - - +
55A ALA 3.5 0.4 - - - -
262A ALA 4.5 1.6 - - - +
263A SER* 3.9 21.8 - - - +
266A PHE* 3.6 55.1 - - + -
280A PHE* 3.9 24.5 - - + -
284A VAL* 4.8 10.8 - - + -
297A ILE* 5.6 0.7 - - + -
298A VAL* 4.3 17.9 - - + -
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Residues in contact with GLY 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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51A SER 3.0 14.1 + - - -
52A LEU 3.2 1.8 + - - -
53A LEU* 1.3 79.1 - - - +
55A ALA* 1.3 59.8 + - - +
56A PRO* 3.2 13.3 - - - +
266A PHE* 5.0 2.2 - - - -
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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