Contacts of the helix formed by residues 57 - 66 (chain A) in PDB entry 3THP
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 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A LEU* 5.1 2.2 - - - -
55A GLY 3.5 5.4 + - - -
56A VAL* 1.3 74.3 - - - +
58A ARG* 1.3 61.9 + - - +
59A ASN* 2.9 22.2 + - - +
60A GLN* 2.9 30.5 + - - +
61A LEU* 3.0 15.1 + - - +
76A MSE 4.6 1.3 - - - -
106A VAL 5.7 0.2 + - - -
107A ASP* 5.7 0.2 - - - +
108A ASP* 6.5 0.9 - - - -
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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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52A LEU* 5.0 3.7 - - + +
56A VAL 4.0 1.4 + - - -
57A SER* 1.3 73.9 + - - +
59A ASN* 1.3 65.9 + - - +
60A GLN 3.2 3.6 + - - -
61A LEU* 4.6 1.1 - - - +
62A LEU* 3.2 30.2 + - + +
74A LEU* 3.0 50.5 + - + +
76A MSE 3.9 41.0 + - - +
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Residues in contact with ASN 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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57A SER* 2.9 10.1 + - - +
58A ARG* 1.3 85.6 + - - +
60A GLN* 1.3 58.3 + - - +
63A PRO* 3.0 22.8 - - - +
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Residues in contact with GLN 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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56A VAL* 4.6 6.9 - - - +
57A SER* 2.9 24.1 + - - +
59A ASN* 1.3 80.5 - - - +
61A LEU* 1.3 67.1 + - - +
63A PRO* 3.4 10.6 - - - +
64A VAL* 3.4 19.0 - - - +
105A VAL* 3.5 31.3 - - - +
106A VAL* 3.2 45.6 + - + +
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Residues in contact with LEU 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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47A VAL* 4.4 8.5 - - + -
50A GLY* 3.1 31.0 - - - +
56A VAL* 4.0 11.0 - - + -
57A SER 3.0 13.0 + - - +
58A ARG* 4.6 0.9 - - - +
60A GLN* 1.3 78.7 - - - +
62A LEU* 1.3 66.6 + - - +
64A VAL* 2.9 21.9 + - + +
65A LEU* 3.0 39.8 + - + +
74A LEU* 4.4 4.9 - - + -
76A MSE 3.9 10.8 - - + -
83A SER* 3.2 14.8 - - - +
105A VAL* 5.5 1.6 - - + -
115A LEU* 4.0 28.0 - - + -
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Residues in contact with LEU 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* 3.2 24.1 + - + +
59A ASN* 5.4 0.2 - - - -
61A LEU* 1.3 77.6 - - - +
63A PRO* 1.4 68.5 - - + +
64A VAL 2.9 1.6 + - - -
65A LEU* 3.2 4.6 + - + -
66A GLU* 3.0 72.7 + - + +
71A VAL* 4.3 19.5 - - + -
74A LEU* 3.7 27.9 - - + +
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Residues in contact with PRO 63 (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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59A ASN* 3.0 33.2 - - - +
60A GLN* 3.4 12.6 - - - +
62A LEU* 1.4 97.9 - - + +
64A VAL* 1.3 58.7 - - + +
66A GLU* 4.2 13.9 + - - +
67A LYS* 4.2 9.2 + - - +
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Residues in contact with VAL 64 (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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60A GLN* 3.4 20.9 - - - +
61A LEU* 2.9 13.3 + - + +
63A PRO* 1.3 77.5 - - + +
65A LEU* 1.3 58.5 + - + +
66A GLU 3.0 1.6 - - - -
67A LYS* 2.6 40.1 + - + +
68A CYS* 4.6 2.4 - - - -
100A LEU* 3.9 29.2 - - + -
103A LYS* 4.4 21.8 - - + +
105A VAL* 4.6 17.3 - - + -
115A LEU* 5.8 2.2 - - + -
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Residues in contact with LEU 65 (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 VAL* 4.4 18.8 - - + -
61A LEU* 3.0 39.7 + - + +
62A LEU* 3.8 6.7 - - + +
64A VAL* 1.3 82.0 - - + +
66A GLU* 1.3 59.2 + - - +
67A LYS 3.1 4.2 + - - -
68A CYS* 3.5 5.0 + - - -
71A VAL* 3.9 12.1 - - + -
74A LEU* 3.9 22.4 - - + -
85A ALA* 3.9 24.7 - - + -
87A TYR* 2.6 37.2 + - + +
100A LEU* 3.7 24.7 - - + -
117A LEU* 4.9 3.4 - - + -
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Residues in contact with GLU 66 (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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62A LEU* 3.0 55.7 + - + +
63A PRO* 4.4 9.8 - - - +
64A VAL 3.0 0.4 + - - -
65A LEU* 1.3 72.5 - - - +
67A LYS* 1.3 55.8 + - - +
68A CYS 3.1 8.8 + - - -
69A GLY 3.6 19.6 + - - +
71A VAL* 3.8 16.0 + - + +
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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