Contacts of the helix formed by residues 51 - 62 (chain A) in PDB entry 2IBS
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 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A GLU* 3.2 14.8 - - - -
48A CYS 2.8 11.2 + - - -
49A ALA 3.3 1.0 + - - -
50A HIS* 1.3 78.3 - - - +
52A PRO* 1.4 68.6 - - - +
53A PHE 3.3 3.1 + - - -
54A LEU* 3.5 4.5 + - - +
55A ARG* 3.2 27.9 + - - +
79A LEU* 3.7 16.3 - - - +
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Residues in contact with PRO 52 (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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23A THR* 5.7 5.8 - - - +
28A VAL* 4.2 12.5 - - + +
45A GLU* 3.4 15.3 - - - +
48A CYS 3.5 5.8 - - - +
50A HIS* 3.7 29.1 - - + +
51A GLY* 1.4 90.5 - - - +
53A PHE* 1.3 70.0 + - + +
55A ARG* 3.7 11.5 + - + +
56A ALA* 3.1 27.7 + - - +
1001A NEA 6.1 1.8 - - - +
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Residues in contact with PHE 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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23A THR* 3.9 24.0 - - + -
28A VAL* 3.8 37.2 - - + -
31A MET* 3.6 42.2 - - + -
32A VAL* 4.5 4.9 - - + +
45A GLU* 3.3 29.6 + - - +
52A PRO* 1.3 83.4 - - + +
54A LEU* 1.3 61.3 + - - +
56A ALA* 4.1 0.7 - - - +
57A PHE* 3.1 29.6 + - - +
103A LEU* 3.8 30.2 - - + +
104A GLY* 3.6 24.7 - - - -
105A ASN* 3.7 9.2 - - + -
1001A NEA 5.8 1.3 - - - -
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Residues in contact with LEU 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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43A VAL* 3.8 23.1 - - + +
44A LEU 4.3 0.2 - - - -
45A GLU* 3.3 28.2 + - + +
48A CYS* 4.9 0.2 - - + -
51A GLY 3.9 4.5 - - - +
52A PRO 3.4 0.4 - - - -
53A PHE* 1.3 74.6 - - - +
55A ARG* 1.3 64.0 + - - +
57A PHE* 4.6 2.2 - - - -
58A ARG* 3.1 24.8 + - - +
67A PHE* 3.8 21.3 - - + -
68A VAL 3.6 34.1 - - - +
69A GLY* 4.2 2.2 - - - +
79A LEU* 3.9 27.6 - - + -
82A TRP* 3.8 15.4 - - + -
83A ALA* 4.4 11.2 - - + -
103A LEU* 4.6 1.8 - - + -
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Residues in contact with ARG 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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50A HIS* 3.0 32.2 + - - +
51A GLY 3.2 13.8 + - - +
52A PRO* 3.8 9.2 - - - +
53A PHE 3.3 0.2 - - - -
54A LEU* 1.3 78.4 - - - +
56A ALA* 1.3 56.4 + - - +
58A ARG* 3.4 2.6 + - - +
59A GLU* 3.0 37.6 + - + +
78A ASP* 3.3 15.8 + - - -
80A PRO* 3.4 19.2 - - + +
82A TRP* 4.0 22.0 - - + -
221D GLN* 3.3 47.5 - - - +
222D GLU* 2.8 32.7 + - - +
223D SER* 4.6 1.0 - - - +
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Residues in contact with ALA 56 (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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28A VAL* 3.8 23.1 - - + -
29A ASP* 4.9 9.0 - - - +
32A VAL* 3.8 12.7 - - + +
52A PRO 3.1 16.7 + - - +
53A PHE 4.1 0.9 - - - +
54A LEU 3.4 0.2 - - - -
55A ARG* 1.3 76.6 - - - +
57A PHE* 1.3 63.9 + - - +
59A GLU* 3.6 6.9 + - - +
60A ALA* 3.2 24.8 + - - +
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Residues in contact with PHE 57 (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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32A VAL* 3.9 10.7 - - + +
35A ALA* 4.0 18.8 - - + -
36A GLU* 4.9 0.2 - - - -
37A ALA* 3.8 18.2 - - + -
43A VAL* 3.9 20.2 - - + -
53A PHE 3.1 19.3 + - - +
54A LEU* 4.0 4.5 - - - +
56A ALA* 1.3 74.5 - - - +
58A ARG* 1.3 59.0 + - - +
60A ALA 3.4 0.2 + - - -
61A HIS* 2.9 62.4 + + + +
65A TYR* 3.8 26.7 - + - -
67A PHE* 3.7 19.7 - + + -
101A LEU* 3.4 29.6 - - + -
103A LEU* 4.4 8.1 - - + -
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Residues in contact with ARG 58 (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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54A LEU 3.1 18.0 + - - +
55A ARG* 3.7 4.9 - - - +
56A ALA 3.3 0.2 - - - -
57A PHE* 1.3 76.0 - - - +
59A GLU* 1.3 60.2 + - + +
62A GLY* 3.0 47.3 + - - +
63A THR* 3.5 34.4 + - + +
67A PHE* 3.7 19.1 - - + -
82A TRP* 3.4 73.6 - - + +
222D GLU* 5.3 2.0 + - - -
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Residues in contact with GLU 59 (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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55A ARG* 3.0 25.0 + - + +
56A ALA* 3.9 7.9 - - - +
57A PHE 3.4 0.2 - - - -
58A ARG* 1.3 77.2 - - + +
60A ALA* 1.3 61.5 + - - +
62A GLY 4.9 0.3 + - - -
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Residues in contact with ALA 60 (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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32A VAL* 3.9 12.1 - - + -
56A ALA 3.2 18.7 + - - +
59A GLU* 1.3 80.1 - - - +
61A HIS* 1.3 78.5 + - + +
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Residues in contact with HIS 61 (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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32A VAL* 3.4 35.4 + - + -
33A SER* 5.4 2.7 + - - -
35A ALA 4.1 9.8 + - - -
36A GLU* 6.4 0.4 - - - -
39A ARG* 5.8 4.0 + - - -
57A PHE* 2.9 51.3 + + + +
60A ALA* 1.3 82.4 - - + +
62A GLY* 1.3 59.5 + - - +
65A TYR* 3.5 32.7 + - + +
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Residues in contact with GLY 62 (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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58A ARG* 3.0 34.8 + - - +
59A GLU 4.7 0.6 + - - -
60A ALA 3.8 0.6 - - - -
61A HIS* 1.3 79.1 - - - +
63A THR* 1.3 63.1 + - - -
64A ALA 3.6 2.2 - - - -
65A TYR* 3.6 13.8 - - - -
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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