Contacts of the helix formed by residues 63 - 71 (chain P) in PDB entry 3Q2K
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 63 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42P CYS* 3.5 11.2 - - - -
44P THR* 4.9 8.1 - - - -
61P PHE* 3.5 1.7 - - - +
62P SER* 1.3 84.7 + - - +
64P LEU* 1.3 64.6 + - - +
65P SER* 3.3 20.1 + - - -
66P ASP* 3.2 25.0 + - - +
67P MET* 3.3 10.2 + - - +
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Residues in contact with LEU 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P VAL* 4.5 8.5 - - + -
42P CYS* 3.5 13.4 - - - -
63P SER* 1.3 72.6 - - - +
65P SER* 1.3 57.6 + - - +
67P MET* 3.2 33.1 + - + +
68P LEU* 2.9 47.2 + - + +
76P LEU* 4.3 2.9 - - + -
88P GLN* 3.6 52.5 - - + +
91P GLU* 2.8 26.2 - - - +
92P VAL* 4.1 11.2 - - + -
500P NAI 5.3 2.9 + - - +
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Residues in contact with SER 65 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63P SER* 3.2 11.0 + - - -
64P LEU* 1.3 72.8 - - - +
66P ASP* 1.3 63.7 + - - +
68P LEU* 3.4 5.8 + - - +
69P ALA* 2.9 28.4 + - - +
91P GLU* 3.6 22.0 + - - -
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Residues in contact with ASP 66 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61P PHE* 3.5 18.6 - - + -
62P SER* 4.2 16.3 + - - -
63P SER* 3.2 22.6 + - - +
65P SER* 1.3 78.9 + - - +
67P MET* 1.3 58.1 + - - +
68P LEU 2.8 4.5 - - - -
69P ALA* 2.7 26.8 + - - -
70P GLN* 2.7 31.1 + - - +
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Residues in contact with MET 67 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15P LEU 4.7 4.5 - - - -
16P VAL* 4.2 6.1 - - + -
40P GLU* 3.7 24.0 - - - +
41P ILE 4.2 11.0 - - - +
42P CYS* 3.6 30.7 - - + -
61P PHE* 3.4 31.6 - - + -
63P SER 3.3 5.2 + - - +
64P LEU* 3.2 37.9 - - + +
66P ASP* 1.3 78.7 - - - +
68P LEU* 1.3 58.8 + - + +
71P GLY* 2.8 29.3 + - - -
76P LEU* 3.6 25.4 - - + -
97P ARG* 4.7 0.7 + - - -
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Residues in contact with LEU 68 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64P LEU* 2.9 42.2 + - + +
65P SER* 3.7 5.4 - - - +
66P ASP 2.7 2.2 + - - -
67P MET* 1.3 80.3 - - + +
69P ALA* 1.3 63.2 + - - +
71P GLY 4.1 0.5 - - - +
76P LEU* 3.2 29.2 - - + -
91P GLU* 3.7 33.9 - - + +
92P VAL* 4.0 7.0 - - - -
95P ALA* 4.1 16.2 - - + +
97P ARG* 2.9 44.0 + - + +
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Residues in contact with ALA 69 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65P SER 2.9 15.9 + - - +
66P ASP* 2.7 11.5 + - - +
68P LEU* 1.3 74.2 - - - +
70P GLN* 1.3 65.3 + - + +
71P GLY 3.8 2.3 + - - +
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Residues in contact with GLN 70 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59P ARG* 3.4 32.8 + - - +
61P PHE* 3.7 12.9 - - + -
66P ASP* 2.7 38.1 + - - +
69P ALA* 1.3 80.3 - - + +
71P GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 71 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40P GLU* 3.0 15.0 - - - -
59P ARG* 4.7 4.0 - - - -
61P PHE* 4.4 7.8 - - - -
67P MET* 2.8 26.0 + - - +
68P LEU 4.1 1.6 - - - +
69P ALA 4.3 2.1 - - - +
70P GLN* 1.3 78.1 - - - +
72P ASN* 1.3 61.5 + - - +
73P ALA 3.9 0.7 - - - -
97P ARG* 3.7 18.0 + - - -
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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