Contacts of the helix formed by residues 65 - 74 (chain A) in PDB entry 1X62
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 CYS 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A CYS* 3.3 3.6 - - - +
47A CYS* 3.8 6.5 - - - -
49A THR* 3.8 11.9 - - + -
51A LEU* 3.6 24.5 - - + -
54A LYS* 5.5 4.5 - - + -
55A GLY 4.5 0.2 - - - -
64A TYR* 1.3 74.9 - - - +
66A GLU* 1.3 54.9 + - - +
67A LYS* 2.5 17.4 + - + +
68A HIS* 2.5 42.5 + - - -
69A ALA* 2.7 9.8 + - - -
401A ZN 2.3 36.8 - - - -
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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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54A LYS* 5.8 7.7 - - + +
55A GLY 4.7 3.0 + - - -
57A PHE* 3.8 41.3 - - + -
64A TYR 3.8 2.6 + - - -
65A CYS* 1.3 69.5 - - - +
67A LYS* 1.3 61.8 + - - +
69A ALA* 4.2 2.7 - - - -
70A ARG* 3.0 40.1 + - + +
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Residues in contact with LYS 67 (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* 5.8 2.2 - - - -
65A CYS* 2.5 20.6 + - + +
66A GLU* 1.3 75.6 - - - +
68A HIS* 1.3 72.6 + - + +
70A ARG* 3.1 14.8 - - - +
71A GLU* 3.1 24.3 - - + +
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Residues in contact with HIS 68 (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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46A ASP* 2.9 44.5 + - + +
47A CYS* 3.5 14.1 - - + -
64A TYR* 4.1 10.8 - - + -
65A CYS* 2.5 12.3 + - - +
67A LYS* 1.3 90.4 - - + +
69A ALA* 1.3 67.8 + - - +
70A ARG 3.2 0.2 - - - -
71A GLU* 2.8 23.3 + - + +
72A ARG* 3.0 18.9 + - + +
401A ZN 2.0 38.8 - - - -
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Residues in contact with ALA 69 (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 PHE* 3.3 42.8 - - + -
59A VAL* 4.3 8.2 - - + +
64A TYR* 3.8 14.1 - - + +
65A CYS 2.7 21.2 + - - +
66A GLU* 4.2 1.1 - - - -
68A HIS* 1.3 71.5 - - - +
70A ARG* 1.3 52.1 + - - +
72A ARG* 2.7 27.1 + - - +
73A VAL* 2.7 21.7 + - - +
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Residues in contact with ARG 70 (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 PHE* 5.3 4.4 - - + -
66A GLU* 3.0 31.8 + - + +
67A LYS* 3.1 17.0 - - - +
69A ALA* 1.3 77.4 - - - +
71A GLU* 1.3 80.4 + - + +
73A VAL* 3.4 11.2 - - - +
74A SER* 2.9 39.2 + - - -
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Residues in contact with GLU 71 (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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67A LYS* 3.1 22.6 - - + +
68A HIS* 2.8 21.6 + - + +
70A ARG* 1.3 88.3 + - + +
72A ARG* 1.3 58.9 + - + +
74A SER 2.4 24.2 - - - +
75A GLY* 4.3 2.6 - - - -
76A PRO* 4.9 4.5 - - - +
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Residues in contact with ARG 72 (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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46A ASP* 4.5 15.9 + - - +
59A VAL* 3.7 17.9 - - + -
60A GLU* 3.8 17.6 + - - -
64A TYR* 3.5 57.2 + - - -
68A HIS* 3.0 14.4 + - + +
69A ALA* 2.7 14.5 + - - +
71A GLU* 1.3 72.3 - - + +
73A VAL* 1.3 65.9 + - - +
74A SER 3.0 5.3 + - - -
75A GLY 4.2 1.4 + - - -
76A PRO 4.2 11.3 - - - +
78A SER* 5.4 4.8 + - - -
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Residues in contact with VAL 73 (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 PHE* 5.7 6.5 - - + -
59A VAL* 4.5 17.6 - - + +
69A ALA* 2.7 25.3 + - + +
70A ARG* 3.2 20.6 - - - +
72A ARG* 1.3 72.7 - - - +
74A SER* 1.3 59.3 + - - +
75A GLY 4.1 0.9 + - - -
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Residues in contact with SER 74 (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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70A ARG* 2.9 20.6 + - - +
71A GLU* 2.4 27.7 - - - +
72A ARG 3.9 0.7 - - - -
73A VAL* 1.3 81.2 - - - +
75A GLY* 1.3 56.5 + - - +
76A PRO* 4.6 0.2 - - - +
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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