Contacts of the helix formed by residues 65 - 79 (chain A) in PDB entry 3C51
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 GLN 65 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU* 3.1 34.6 - - - +
60A GLY* 3.0 25.1 + - - +
61A MET* 3.6 9.5 + - - +
63A LEU 5.1 0.2 - - - -
64A GLU* 1.3 77.9 - - + +
66A PRO* 1.4 58.3 - - - +
67A ILE 3.4 0.4 - - - -
68A GLY* 3.0 5.2 + - - +
69A LYS* 2.7 35.6 + - - +
171A PHE* 3.7 4.0 - - - -
175A LYS* 3.1 29.8 + - - +
512A PRO* 4.8 5.8 - - + +
513A ILE* 4.2 12.3 - - + -
516A GLN* 3.2 23.6 + - - +
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Residues in contact with PRO 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLU 3.4 8.7 - - - +
65A GLN* 1.4 81.7 - - - +
67A ILE* 1.3 57.3 + - - +
69A LYS* 3.5 7.0 + - + +
70A ARG* 2.9 28.9 + - - +
513A ILE* 3.9 20.4 - - + +
516A GLN* 3.4 25.4 - - + +
517A GLU* 3.7 29.8 - - + +
520A ILE* 3.9 14.5 - - + +
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Residues in contact with ILE 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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65A GLN 3.4 0.2 - - - -
66A PRO* 1.3 77.6 - - - +
68A GLY* 1.3 57.0 + - - +
70A ARG* 3.1 6.0 + - - +
71A LEU* 2.7 56.3 + - + +
171A PHE* 4.4 5.2 - - + -
174A TRP* 3.4 39.5 - - + -
515A TRP* 4.8 1.1 - - + -
516A GLN* 3.5 32.0 + - + +
519A MET* 4.6 7.4 - - + -
520A ILE* 4.2 11.0 - - + -
525A PHE* 3.3 36.1 - - + -
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Residues in contact with GLY 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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61A MET* 3.3 23.1 - - - -
62A CYS* 4.0 2.7 - - - -
65A GLN* 3.0 4.6 + - - +
67A ILE* 1.3 75.3 - - - +
69A LYS* 1.3 58.7 + - - +
71A LEU* 4.2 1.9 - - - +
72A PHE* 2.8 34.0 + - - +
162A PHE* 4.8 1.7 - - - -
171A PHE* 3.7 26.5 - - - -
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Residues in contact with LYS 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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61A MET 3.6 0.4 + - - -
62A CYS* 2.9 23.3 + - - +
63A LEU 4.0 16.3 + - - +
65A GLN 2.7 20.9 + - - +
66A PRO* 3.7 6.7 - - + +
68A GLY* 1.3 72.2 - - - +
70A ARG* 1.3 63.5 + - - +
72A PHE* 3.9 1.5 - - - +
73A GLN* 3.0 52.1 + - - +
89A TRP* 3.9 9.8 - - + -
93A GLU* 2.9 38.3 + - - -
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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
----------------------------------------------------------
66A PRO 2.9 18.7 + - - +
67A ILE* 3.1 13.4 + - - +
69A LYS* 1.3 76.2 - - - +
71A LEU* 1.3 58.1 + - - +
73A GLN* 3.0 9.1 + - - +
74A GLN* 2.8 42.0 + - - +
77A ARG* 5.8 3.6 - - - +
520A ILE* 3.4 44.8 - - + +
525A PHE* 3.4 31.1 - - + -
532B ARG* 5.2 4.9 - - - +
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Residues in contact with LEU 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 ILE* 2.7 37.6 + - + +
68A GLY 4.2 1.6 - - - +
70A ARG* 1.3 72.4 - - - +
72A PHE* 1.3 62.8 + - - +
74A GLN* 3.2 28.0 + - - +
75A PHE* 3.0 22.3 + - - +
162A PHE* 3.9 11.1 - - + -
167A TYR* 3.9 25.0 - - + +
170A ARG* 3.9 17.0 - - + +
171A PHE* 3.5 38.8 - - + +
174A TRP* 4.3 2.2 - - + -
525A PHE* 4.3 2.5 - - + -
529A ASN* 3.7 15.9 - - - +
531B TRP* 4.4 0.4 - - + -
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Residues in contact with PHE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 4.1 11.7 - + - -
62A CYS* 3.6 34.3 - - + -
68A GLY 2.8 23.6 + - - +
69A LYS 3.9 2.0 - - - +
71A LEU* 1.3 72.9 - - - +
73A GLN* 1.3 56.2 + - - +
75A PHE* 3.3 5.2 - - - +
76A LEU* 3.0 61.7 + - + +
89A TRP* 3.5 27.8 - + - -
154A LEU* 3.7 24.5 - - + -
158A PRO 4.3 0.2 - - - -
159A PHE* 3.9 23.3 - + - -
162A PHE* 3.6 29.5 - + + -
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Residues in contact with GLN 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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69A LYS* 3.0 49.5 + - - +
70A ARG* 3.6 5.9 - - - +
72A PHE* 1.3 73.2 - - - +
74A GLN* 1.3 56.6 + - - +
75A PHE 3.1 2.0 - - - -
76A LEU* 3.6 2.9 - - - +
77A ARG* 2.7 42.9 + - - +
86A LEU* 3.6 23.7 - - + +
89A TRP* 3.3 42.2 - - + -
90A LYS* 4.3 16.4 - - - +
93A GLU* 4.6 3.8 + - - -
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Residues in contact with GLN 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* 2.8 40.6 + - + +
71A LEU* 3.3 29.2 - - - +
73A GLN* 1.3 73.2 - - - +
75A PHE* 1.3 61.6 + - - +
77A ARG* 3.4 34.6 + - - +
78A THR* 3.0 28.2 + - - +
167A TYR* 4.1 11.4 - - + -
525A PHE* 3.9 1.8 - - - -
529A ASN* 2.9 33.0 + - - +
531B TRP* 3.7 19.4 + - - +
532B ARG* 4.2 9.8 - - - +
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Residues in contact with PHE 75 (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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71A LEU 3.0 9.8 + - - +
72A PHE 3.3 7.9 - - - +
74A GLN* 1.3 72.4 - - - +
76A LEU* 1.3 87.1 + - + +
77A ARG 2.9 1.3 - - - -
78A THR* 2.9 17.5 + - - -
79A HIS* 3.1 56.9 + + - +
82A HIS* 3.6 19.1 - + - -
158A PRO 3.6 19.1 - - - -
161A GLU* 3.7 30.7 - - + -
162A PHE* 3.8 26.5 - + + -
165A SER* 4.3 10.5 - - - -
167A TYR* 3.4 27.9 - + + -
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Residues in contact with LEU 76 (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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72A PHE* 3.0 39.0 + - + +
73A GLN* 3.2 6.0 + - - +
75A PHE* 1.3 91.7 - - + +
77A ARG* 1.3 56.8 + - - +
79A HIS 2.9 23.2 - - - +
82A HIS* 3.6 39.7 - - + +
83A GLY* 4.0 4.9 + - - -
86A LEU* 4.0 24.0 - - + +
89A TRP* 4.0 9.9 - - + -
154A LEU* 3.4 35.7 - - + -
158A PRO* 4.1 8.1 - - + -
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Residues in contact with ARG 77 (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* 5.5 3.8 + - - +
73A GLN* 2.7 25.7 + - - +
74A GLN* 3.4 38.6 - - - +
75A PHE 2.9 0.2 - - - -
76A LEU* 1.3 76.2 - - - +
78A THR* 1.3 61.5 + - - +
79A HIS 3.4 5.2 + - - +
80A GLU* 5.4 0.5 - - - -
83A GLY* 5.5 2.6 - - - -
86A LEU* 3.4 21.0 - - + +
90A LYS* 5.3 8.9 - - - +
532B ARG* 3.3 35.0 - - - +
533B PRO* 3.5 38.5 + - + +
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Residues in contact with THR 78 (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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74A GLN 3.0 10.4 + - - +
75A PHE 3.0 12.1 + - - -
77A ARG* 1.3 75.8 - - - +
79A HIS* 1.3 72.4 + - - +
80A GLU 4.0 1.2 + - - -
167A TYR* 2.9 32.7 + - - +
530B VAL* 4.1 13.9 - - + +
531B TRP 3.3 16.8 - - - +
533B PRO* 3.7 22.9 - - + -
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Residues in contact with HIS 79 (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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75A PHE* 3.1 45.8 + + - +
76A LEU 2.9 18.2 - - - +
77A ARG 3.7 4.0 - - - +
78A THR* 1.3 99.7 + - - +
80A GLU* 1.3 64.1 + - - +
81A GLN* 3.4 24.1 + - - +
82A HIS* 3.7 12.7 + - + -
83A GLY* 3.5 6.4 + - - -
161A GLU* 5.2 1.1 - - - -
165A SER* 5.7 0.2 - - - -
167A TYR* 4.2 7.4 - + - -
41B LEU 5.7 3.7 + - - -
565B BR 4.5 15.2 - - + +
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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