Contacts of the helix formed by residues 74 - 88 (chain A) in PDB entry 5M7T
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 VAL 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ARG* 6.4 1.6 - - + -
72A PRO 4.8 4.9 - - - +
73A TRP* 1.3 77.3 - - - +
75A MET* 1.3 66.3 + - - +
76A GLU* 3.9 17.0 - - + +
77A GLN* 3.0 36.1 + - + +
78A ARG* 3.1 12.7 + - - +
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Residues in contact with MET 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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74A VAL* 1.3 73.9 - - - +
76A GLU* 1.3 62.7 + - - +
78A ARG* 3.3 25.2 + - - +
79A LYS* 3.1 39.9 + - - +
118A GLN* 4.1 42.4 - - + +
119A LEU* 5.0 8.3 - - - -
122A LEU* 3.1 53.8 - - + -
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Residues in contact with GLU 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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74A VAL* 3.3 12.2 - - + +
75A MET* 1.3 77.5 - - - +
77A GLN* 1.3 63.6 + - + +
79A LYS* 3.4 12.5 + - - +
80A GLU* 3.1 22.0 + - + +
395A HIS* 3.7 23.9 + - + -
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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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72A PRO 4.7 0.5 - - - +
73A TRP* 3.3 15.5 - - + +
74A VAL* 3.0 39.7 + - + +
76A GLU* 1.3 76.7 - - + +
78A ARG* 1.3 61.4 + - - +
80A GLU* 3.2 5.0 + - - +
81A LEU 2.8 23.7 + - - -
318A PHE* 3.1 59.0 - - + +
319A GLU* 5.3 2.4 + - - +
635A THR* 6.0 3.2 - - - +
639A ASP* 4.8 6.5 + - - -
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Residues in contact with ARG 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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66A GLU* 2.8 43.1 + - - +
72A PRO* 3.7 2.0 - - - +
73A TRP* 3.0 29.9 + - + -
74A VAL* 3.1 13.8 + - - +
75A MET* 3.5 40.0 - - - +
77A GLN* 1.3 77.5 - - - +
79A LYS* 1.3 60.9 + - - +
81A LEU* 3.3 8.2 + - - +
82A PHE* 3.1 33.4 + - + -
93A TYR* 3.4 14.8 + - + +
95A TYR* 3.6 23.4 + - - -
97A PRO* 3.7 3.0 - - - +
100A ASP* 3.4 22.2 + - - -
119A LEU* 5.9 0.2 - - - +
122A LEU* 3.7 22.6 - - + +
318A PHE* 5.2 0.7 - - - -
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Residues in contact with LYS 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 MET* 3.1 39.1 + - - +
76A GLU* 3.6 11.0 - - - +
78A ARG* 1.3 74.8 - - - +
80A GLU* 1.3 62.7 + - - +
82A PHE* 3.2 12.4 + - - +
83A ARG* 3.1 20.1 + - - +
118A GLN* 4.7 3.0 + - - -
121A THR* 3.7 33.2 - - - +
122A LEU* 4.0 19.0 - - + +
125A ALA* 4.0 20.0 - - + -
129A TYR* 4.2 9.9 - - + -
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Residues in contact with GLU 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 GLU* 3.1 13.9 + - + +
77A GLN* 3.2 10.5 + - - +
79A LYS* 1.3 76.2 - - - +
81A LEU* 1.3 62.6 + - - +
83A ARG* 3.2 44.3 + - - +
84A ARG* 2.8 55.9 + - - +
318A PHE* 3.9 13.5 - - + -
319A GLU* 5.6 1.1 - - - +
395A HIS* 6.0 6.3 - - + -
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Residues in contact with LEU 81 (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 VAL* 3.8 17.3 - - + -
73A TRP* 3.8 23.6 - - + -
77A GLN 2.8 13.9 + - - +
78A ARG* 3.3 11.6 + - - +
80A GLU* 1.3 73.0 - - - +
82A PHE* 1.3 61.4 + - + +
84A ARG* 3.0 10.7 + - + +
85A LEU* 2.8 45.1 + - + +
93A TYR* 3.6 33.2 - - + -
318A PHE* 3.8 17.8 - - + -
325A ILE* 3.7 29.8 - - + -
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Residues in contact with PHE 82 (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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78A ARG* 3.1 14.0 + - + -
79A LYS* 3.2 7.6 + - - +
81A LEU* 1.3 77.5 - - + +
83A ARG* 1.3 63.0 + - - +
85A LEU* 3.3 4.7 + - + +
86A GLN* 3.0 24.8 + - - +
93A TYR* 3.6 49.8 - + + -
122A LEU* 3.4 48.9 - - + -
125A ALA* 3.9 9.4 - - + -
126A ALA* 3.7 31.4 - - + -
129A TYR* 3.8 19.6 - + + +
131A ILE* 3.9 18.4 - - + +
133A PHE* 4.1 1.8 - + - -
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Residues in contact with ARG 83 (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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79A LYS 3.1 9.6 + - - +
80A GLU* 3.2 43.7 + - - +
81A LEU 3.2 0.2 - - - -
82A PHE* 1.3 79.6 - - - +
84A ARG* 1.3 70.9 + - - +
86A GLN* 3.4 3.6 + - - +
87A LYS* 3.2 41.5 + - - +
129A TYR* 4.0 35.5 - - + +
390A GLU* 5.6 6.9 + - - -
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Residues in contact with ARG 84 (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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80A GLU* 2.8 46.8 + - - +
81A LEU* 3.0 16.5 + - + +
83A ARG* 1.3 81.6 - - - +
85A LEU* 1.3 67.5 + - - +
87A LYS* 3.2 8.0 + - + +
88A TRP* 3.1 60.9 + - + -
318A PHE* 4.2 13.4 + - - -
319A GLU* 3.0 35.6 + - - +
321A ASN 5.3 0.8 - - - -
322A TYR* 3.6 37.4 - - + +
325A ILE* 5.9 3.0 - - + +
387A TRP* 5.8 0.2 - - - +
390A GLU* 5.4 7.4 + - - +
395A HIS* 6.3 0.2 - - - -
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Residues in contact with LEU 85 (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 GLY* 4.3 3.8 - - - -
64A VAL* 4.0 14.4 - - + +
81A LEU* 2.8 36.6 + - + +
82A PHE* 3.6 8.1 - - + +
84A ARG* 1.3 76.9 - - - +
86A GLN* 1.3 61.4 + - - +
88A TRP* 3.4 2.0 + - - -
89A GLU 3.1 3.3 + - - -
90A LEU* 2.9 65.6 + - + +
92A THR 3.6 22.2 - - - +
93A TYR* 4.4 6.5 - - + -
131A ILE* 3.7 25.8 - - + -
325A ILE* 3.9 13.7 - - + -
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Residues in contact with GLN 86 (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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82A PHE 3.0 14.0 + - - +
83A ARG* 3.8 5.2 - - - +
84A ARG 3.2 0.2 - - - -
85A LEU* 1.3 77.7 - - - +
87A LYS* 1.3 63.3 + - - +
89A GLU* 3.1 15.2 + - - +
90A LEU 4.4 2.9 - - - -
128A GLU 4.7 2.6 + - - -
129A TYR* 3.3 54.5 + - + +
130A GLU* 3.8 20.8 + - + +
131A ILE* 4.0 4.9 - - - +
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Residues in contact with LYS 87 (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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83A ARG* 3.2 31.5 + - - +
84A ARG* 3.5 11.0 - - + +
86A GLN* 1.3 79.2 + - - +
88A TRP* 1.3 77.2 + - + +
89A GLU* 3.6 6.4 + - - +
322A TYR* 4.4 4.8 + - - -
386A GLU* 3.4 30.0 + - - +
390A GLU* 5.6 3.2 + - - -
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Residues in contact with TRP 88 (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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84A ARG* 3.1 43.8 + - + +
85A LEU* 4.2 2.7 - - - +
86A GLN 3.1 0.2 - - - -
87A LYS* 1.3 96.7 - - + +
89A GLU* 1.3 68.2 + - - +
90A LEU* 3.2 3.6 + - + +
322A TYR* 3.5 56.3 - + - -
325A ILE* 3.7 36.3 - - + -
326A HIS* 3.6 30.6 - + - -
329A ALA* 3.5 21.1 - - + +
333A LYS* 3.0 27.2 + - - +
386A GLU* 3.0 21.6 + - - -
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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