Contacts of the helix formed by residues 67 - 80 (chain A) in PDB entry 5V5Z
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 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A SER* 3.2 15.1 + - - +
66A GLN* 1.3 87.7 + - + +
68A PRO* 1.3 65.6 - - - +
69A TYR 3.5 2.0 - - - -
70A GLU* 3.4 35.4 - - + +
71A PHE* 3.2 18.5 + - - +
502A ASP* 5.8 2.4 + - - +
503A PRO* 4.0 18.5 + - - +
505A TYR* 3.6 19.8 + - - -
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Residues in contact with PRO 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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64A TYR* 3.0 40.8 - - + +
67A GLN* 1.3 85.0 - - - +
69A TYR* 1.3 70.6 + - + +
71A PHE* 3.7 7.4 - - + -
72A PHE* 2.8 40.3 + - + -
377A HIS* 4.3 21.3 - - + +
505A TYR* 3.6 38.6 - - + +
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Residues in contact with TYR 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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68A PRO* 1.3 80.9 - - + +
70A GLU* 1.3 67.2 + - + +
72A PHE* 3.2 15.5 + + - +
73A GLU* 2.9 21.8 + - - +
374A MET* 4.6 7.6 + - - +
376A LEU 4.4 1.7 + - - -
377A HIS* 3.2 34.3 - - + +
405A SER* 3.8 10.1 - - - -
407A GLY* 3.5 19.4 - - - -
408A TYR* 3.2 43.0 - - + -
411A THR* 4.9 10.8 - - - +
505A TYR* 4.2 25.8 - + - -
510A VAL* 6.3 0.2 - - + -
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Residues in contact with GLU 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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67A GLN* 3.4 44.4 - - + +
69A TYR* 1.3 74.5 - - + +
71A PHE* 1.3 55.2 + - - +
73A GLU* 2.8 9.6 + - - +
74A SER* 2.7 40.8 + - - +
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Residues in contact with PHE 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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51A VAL* 4.2 7.9 - - + -
60A SER* 3.6 33.7 - - - -
63A SER* 3.0 37.5 - - - +
64A TYR* 4.0 17.0 - + + -
67A GLN 3.2 18.0 + - - +
68A PRO* 3.6 6.1 - - + +
69A TYR 3.3 0.2 - - - -
70A GLU* 1.3 77.6 - - - +
72A PHE* 1.3 72.6 + + - +
74A SER* 3.5 9.0 + - - -
75A CYS* 2.9 52.3 + - - -
83A PHE* 5.2 0.2 - + - -
85A PHE* 3.9 33.9 - + + -
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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
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64A TYR* 4.1 28.9 - + - -
68A PRO* 2.8 29.2 + - + +
69A TYR* 3.4 25.6 - + - +
70A GLU 3.1 0.4 - - - -
71A PHE* 1.3 85.2 - + - +
73A GLU* 1.3 56.6 + - - +
75A CYS* 3.2 5.4 + - - +
76A ARG* 2.9 27.4 + - - +
83A PHE* 3.9 17.8 - + - -
85A PHE* 4.5 9.6 - + - -
94A VAL* 4.2 12.8 - - + -
96A LEU* 4.1 17.4 - - + +
377A HIS* 4.8 3.4 - - - -
378A SER* 4.7 2.2 - - - -
403A LEU* 4.2 18.8 - - + -
405A SER* 3.5 24.9 - - - -
408A TYR* 4.0 14.4 - - + -
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Residues in contact with GLU 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 TYR 2.9 11.5 + - - +
70A GLU* 2.8 11.9 + - - +
72A PHE* 1.3 71.1 - - - +
74A SER* 1.3 51.6 + - - +
75A CYS 2.6 6.6 + - - -
76A ARG* 2.6 52.7 + - - +
77A GLN* 2.8 33.4 + - - +
408A TYR* 2.7 31.7 + - + -
412A SER* 4.7 3.5 + - - -
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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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63A SER* 6.0 0.4 - - - -
70A GLU* 2.7 22.8 + - - +
71A PHE* 3.6 14.1 - - - -
73A GLU* 1.3 69.6 - - - +
75A CYS* 1.3 58.8 + - - +
77A GLN* 3.4 18.9 + - - +
78A LYS* 3.1 36.9 + - - +
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Residues in contact with CYS 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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51A VAL* 3.5 30.7 - - + -
71A PHE* 2.9 45.9 + - - -
72A PHE 3.2 8.0 + - - +
73A GLU 2.6 5.2 + - - -
74A SER* 1.3 78.7 - - - +
76A ARG* 1.3 58.8 + - - +
77A GLN 3.5 0.9 - - - -
78A LYS* 3.8 5.2 - - - -
79A TYR* 2.7 35.7 + - + +
80A GLY 4.1 0.8 - - - +
83A PHE* 3.4 24.4 - - + -
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Residues in contact with ARG 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 2.9 12.7 + - - +
73A GLU* 2.6 39.6 + - - +
75A CYS* 1.3 69.6 - - - +
77A GLN* 1.3 63.0 + - - +
78A LYS 3.0 1.5 - - - -
80A GLY* 2.9 44.5 + - - +
81A ASP* 3.6 14.9 + - - -
83A PHE* 4.7 0.2 - - - -
96A LEU* 4.1 10.1 - - + -
408A TYR* 3.1 18.4 + - - -
414A ARG* 2.9 51.1 - - - +
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Residues in contact with GLN 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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73A GLU* 2.8 28.1 + - + +
74A SER* 3.4 26.3 + - - +
76A ARG* 1.3 78.5 - - - +
78A LYS* 1.3 84.3 + - + +
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Residues in contact with LYS 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 SER* 3.1 33.8 + - - +
75A CYS* 3.8 0.7 - - - +
76A ARG 3.0 0.4 - - - -
77A GLN* 1.3 100.1 + - + +
79A TYR* 1.3 86.0 + - + +
80A GLY 3.8 0.7 - - - -
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Residues in contact with TYR 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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49A PRO* 3.3 34.0 - - + +
50A LEU 3.5 21.4 + - - -
51A VAL* 4.1 23.1 - - + -
52A PHE* 4.7 3.1 + - - +
75A CYS* 2.7 32.0 + - + +
78A LYS* 1.3 94.3 - - + +
80A GLY* 1.3 61.6 + - - +
81A ASP 3.9 0.2 + - - -
82A VAL 3.5 10.6 + - - +
83A PHE* 4.0 22.2 - - + -
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Residues in contact with GLY 80 (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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76A ARG* 2.9 35.6 + - - +
78A LYS 3.8 0.4 - - - -
79A TYR* 1.3 81.3 - - - +
81A ASP* 1.3 64.7 + - - -
83A PHE* 3.4 15.4 - - - -
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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