Contacts of the helix formed by residues 49 - 60 (chain A) in PDB entry 2D7L
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 SER 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A LEU* 1.3 72.5 - - - +
50A THR* 1.3 57.0 + - - +
51A GLU* 2.5 29.0 + - - +
52A GLU* 2.6 47.2 + - - -
53A ARG* 3.0 9.8 + - - +
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Residues in contact with THR 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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48A LEU 3.5 3.0 + - - -
49A SER* 1.3 72.8 + - - +
51A GLU* 1.3 62.5 + - + +
53A ARG* 4.2 26.2 + - - +
54A LYS* 3.5 22.5 + - + +
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Residues in contact with GLU 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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49A SER* 2.5 16.0 + - - +
50A THR* 1.3 78.7 - - + +
52A GLU* 1.3 56.7 + - + +
53A ARG 3.2 1.8 - - - -
54A LYS* 3.0 16.0 + - + +
55A VAL* 2.6 45.5 + - + +
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Residues in contact with GLU 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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16A TRP* 5.3 0.9 + - - -
48A LEU* 3.2 27.0 - - + +
49A SER* 2.6 45.6 + - - +
51A GLU* 1.3 74.8 - - + +
53A ARG* 1.3 56.0 + - - +
55A VAL* 4.1 6.1 - - - -
56A TRP* 2.8 51.4 + - + +
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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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45A PHE* 4.2 24.3 - - + +
46A ARG* 3.4 20.7 + - - +
48A LEU* 3.7 32.5 + - + +
49A SER 3.0 10.9 + - - +
50A THR* 4.2 26.8 + - - +
52A GLU* 1.3 78.7 - - - +
54A LYS* 1.3 65.3 + - - +
56A TRP* 3.2 3.2 + - - +
57A ALA* 2.9 24.3 + - - +
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Residues in contact with LYS 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 THR* 3.5 16.9 + - + +
51A GLU* 3.0 30.2 + - + +
53A ARG* 1.3 79.1 - - - +
55A VAL* 1.3 75.8 + - - +
57A ALA* 3.4 7.8 + - - +
58A ASN* 2.7 44.5 + - - +
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Residues in contact with VAL 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 GLU* 2.6 37.2 + - + +
52A GLU* 3.5 7.0 - - - +
54A LYS* 1.3 87.6 - - - +
56A TRP* 1.3 60.1 + - + +
57A ALA 3.0 1.1 - - - -
58A ASN* 2.6 30.1 + - - +
59A LYS* 2.9 46.2 + - + +
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Residues in contact with TRP 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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12A GLY* 3.2 26.4 - - - +
15A MET* 3.7 39.9 - - + +
16A TRP* 3.4 30.4 - + + -
19A GLU* 4.0 26.2 - - + -
20A ASN* 4.5 4.0 - - - -
45A PHE* 4.2 3.8 - - + -
48A LEU* 3.9 15.3 - - + -
52A GLU* 2.8 49.0 + - + +
53A ARG 3.8 2.7 - - - +
55A VAL* 1.3 74.2 - - + +
57A ALA* 1.3 61.5 + - - +
59A LYS* 3.4 41.2 - - + +
60A ALA* 3.3 18.5 + - - +
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Residues in contact with ALA 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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11A THR* 5.8 0.5 - - - -
12A GLY* 3.8 17.3 + - - +
45A PHE* 6.1 0.7 - - + -
53A ARG 2.9 18.0 + - - +
54A LYS* 3.5 10.1 - - - +
56A TRP* 1.3 76.9 - - - +
58A ASN* 1.3 60.1 + - - +
60A ALA* 4.4 2.0 - - - +
61A LYS* 3.4 28.0 + - - +
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Residues in contact with ASN 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 LYS* 2.7 39.4 + - - +
55A VAL* 2.6 17.4 + - - +
57A ALA* 1.3 72.8 - - - +
59A LYS* 1.3 63.5 + - + +
60A ALA 3.5 0.2 - - - -
61A LYS* 3.3 35.3 - - - +
63A GLU* 3.5 17.7 - - - +
64A THR* 5.7 9.8 - - + +
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Residues in contact with LYS 59 (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 MET* 3.6 22.9 - - + +
55A VAL* 2.9 40.3 + - + +
56A TRP* 3.3 51.1 + - + +
58A ASN* 1.3 74.9 - - + +
60A ALA* 1.3 65.0 + - - +
61A LYS 3.0 2.6 + - - -
62A GLY* 3.2 15.1 + - - -
63A GLU 5.2 1.3 - - - -
64A THR 5.7 2.5 - - - +
65A ALA* 4.9 12.4 - - + +
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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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9A PRO* 5.8 0.7 - - - +
10A LYS* 3.3 41.1 + - + +
11A THR* 3.3 28.0 - - - +
12A GLY 4.0 0.7 - - - +
15A MET* 3.6 18.5 - - + +
56A TRP 3.3 6.8 + - - +
57A ALA 4.6 2.0 - - - +
58A ASN 3.5 0.2 - - - -
59A LYS* 1.3 80.0 - - - +
61A LYS* 1.3 66.2 + - - +
62A GLY* 3.3 1.2 + - - -
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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