Contacts of the helix formed by residues 74 - 96 (chain A) in PDB entry 6DMY
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 LYS 74 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ARG* 1.3 93.0 - - + +
75A ALA* 1.3 65.9 + - + +
76A PRO* 3.7 1.1 - - - -
77A LEU* 4.3 5.9 + - - +
78A TRP* 3.7 18.4 + - - +
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Residues in contact with ALA 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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73A ARG 4.4 0.6 - - - +
74A LYS* 1.3 82.8 - - + +
76A PRO* 1.4 65.0 - - + +
77A LEU 3.3 0.4 - - - -
78A TRP* 3.2 11.0 + - + +
79A LEU* 2.9 41.9 + - + +
1048A LEU* 5.5 3.8 - - + -
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Residues in contact with PRO 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG 3.9 20.0 - - - +
74A LYS 4.0 1.6 - - - +
75A ALA* 1.4 92.1 - - + +
77A LEU* 1.3 61.6 + - + +
79A LEU* 3.9 5.5 - - + +
80A ARG* 3.0 37.4 + - - +
1048A LEU* 3.8 39.0 - - + +
1049A ASN* 5.5 8.7 - - + +
1105A LEU* 6.4 2.0 - - + -
1183A GLU* 6.2 3.1 - - + -
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG 4.4 15.5 - - - +
74A LYS* 4.3 6.8 + - - +
75A ALA 3.3 0.8 - - - -
76A PRO* 1.3 78.0 - - + +
78A TRP* 1.3 60.5 + - - +
80A ARG* 3.7 12.6 + - - +
81A ALA* 3.0 27.2 + - - +
1183A GLU* 2.5 72.9 - - + +
1184A VAL* 5.4 0.4 - - - -
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Residues in contact with TRP 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 LYS 3.7 14.0 + - - +
75A ALA* 3.2 13.7 + - + +
77A LEU* 1.3 78.4 - - - +
79A LEU* 1.3 85.7 + - + +
81A ALA* 3.3 11.3 - - + +
82A LYS* 2.9 55.6 + - - +
85A ARG* 5.4 4.6 - - - +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA* 2.9 26.0 + - + +
76A PRO* 3.9 4.7 - - + +
77A LEU 3.3 0.2 - - - -
78A TRP* 1.3 104.2 - - + +
80A ARG* 1.3 60.9 + - + +
82A LYS* 3.0 13.1 + - + +
83A PHE* 2.9 43.1 + - + -
1048A LEU* 3.7 30.7 - - + -
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Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PRO* 3.0 24.5 + - + +
77A LEU* 3.7 13.1 + - - +
79A LEU* 1.3 71.9 - - - +
81A ALA* 1.3 59.6 + - - +
83A PHE* 3.4 11.9 + - + +
84A GLN* 3.0 58.3 + - - +
1046A PHE 5.8 3.4 - - - +
1047A LEU* 5.9 10.3 - - - +
1048A LEU 6.0 1.6 - - - +
1102A LEU* 5.4 8.4 - - - +
1105A LEU* 5.6 10.1 - - - -
1106A THR* 3.9 23.0 - - - +
1183A GLU* 2.6 34.7 + - - -
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Residues in contact with ALA 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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77A LEU 3.0 18.9 + - - +
78A TRP* 3.3 15.9 - - + +
79A LEU 3.2 0.2 - - - -
80A ARG* 1.3 77.3 - - - +
82A LYS* 1.3 56.1 + - - +
84A GLN* 4.0 7.3 - - - +
85A ARG* 2.9 38.3 + - + +
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Residues in contact with LYS 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 TRP* 2.9 47.3 + - + +
79A LEU* 3.0 19.7 + - + +
81A ALA* 1.3 75.3 - - - +
83A PHE* 1.3 64.2 + - - +
85A ARG* 3.7 39.8 - - + +
86A LEU* 4.2 22.2 + - + +
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Residues in contact with PHE 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 LEU* 2.9 40.0 + - + -
80A ARG* 3.8 12.8 - - + +
81A ALA 3.3 0.2 - - - -
82A LYS* 1.3 79.4 - - + +
84A GLN* 1.3 63.1 + - + +
85A ARG 3.6 0.2 + - - -
86A LEU* 4.0 1.9 + - - +
87A LEU* 3.6 21.8 + - - +
546A ALA* 5.2 17.7 - - + -
1045A VAL* 4.1 26.7 - - + -
1046A PHE* 4.6 28.0 - + - -
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Residues in contact with GLN 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 ARG* 3.0 45.7 + - + +
81A ALA* 3.4 8.1 + - - +
83A PHE* 1.3 80.6 - - + +
85A ARG* 1.3 57.9 + - - +
87A LEU* 3.4 2.9 + - - -
88A PHE* 3.0 32.7 + - - +
542A LYS* 3.7 50.3 + - + +
543A ARG* 5.0 5.1 - - - +
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Residues in contact with ARG 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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78A TRP* 5.4 4.9 - - - +
81A ALA* 2.9 21.6 + - + +
82A LYS* 3.7 42.4 - - + +
84A GLN* 1.3 75.9 - - - +
86A LEU* 1.3 71.9 + - + +
88A PHE* 4.3 10.4 - - - +
89A LYS* 4.0 13.7 + - - +
542A LYS* 5.7 0.4 - - - -
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Residues in contact with LEU 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 LYS* 4.2 24.7 - - + +
83A PHE 4.0 3.2 + - - +
84A GLN 3.2 0.2 - - - -
85A ARG* 1.3 91.1 - - + +
87A LEU* 1.3 59.8 + - - +
88A PHE 3.2 1.8 - - - -
89A LYS* 3.0 24.7 + - + +
90A LEU* 3.0 24.8 + - - +
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Residues in contact with LEU 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 PHE 3.6 18.2 + - - +
84A GLN* 3.4 3.5 + - - +
86A LEU* 1.3 76.1 - - - +
88A PHE* 1.3 59.8 + - - +
90A LEU* 3.5 24.8 + - + -
91A GLY* 3.0 22.0 + - - -
538A GLY 4.6 0.7 - - - +
541A LEU* 3.3 47.8 - - + +
542A LYS* 3.8 8.3 - - - +
545A GLY* 4.5 12.1 - - - -
546A ALA 5.8 0.7 - - - +
589A LEU* 4.7 16.6 - - + -
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Residues in contact with PHE 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 GLN 3.0 18.3 + - - +
85A ARG* 4.3 9.9 - - - +
87A LEU* 1.3 75.8 - - - +
89A LYS* 1.3 62.6 + - + +
91A GLY* 3.0 3.8 + - - -
92A CYS* 2.9 48.6 + - - -
535A ASP* 3.1 47.8 - - - -
538A GLY* 3.5 25.4 - - - -
539A GLU* 4.0 1.1 - - + -
542A LYS* 4.0 21.5 - - + +
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Residues in contact with LYS 89 (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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85A ARG 4.0 7.5 + - - +
86A LEU* 3.0 28.9 + - + +
88A PHE* 1.3 78.0 - - + +
90A LEU* 1.3 60.0 + - - +
92A CYS* 3.0 26.1 + - + +
93A TYR* 3.0 17.3 + - + +
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Residues in contact with LEU 90 (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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86A LEU 3.0 11.7 + - - +
87A LEU* 3.5 30.1 - - + +
89A LYS* 1.3 74.8 - - - +
91A GLY* 1.3 57.0 + - - +
93A TYR* 3.5 10.7 + - + +
94A ILE* 2.9 52.6 + - + +
541A LEU* 5.0 4.0 - - + -
589A LEU* 4.7 5.6 - - + -
590A LEU* 4.3 24.2 - - + -
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Residues in contact with GLY 91 (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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87A LEU 3.0 13.9 + - - -
88A PHE 3.0 6.4 + - - -
90A LEU* 1.3 77.2 - - - +
92A CYS* 1.3 55.1 + - - +
94A ILE* 4.5 1.1 - - - -
95A GLN* 2.9 28.2 + - - +
537A THR* 3.8 9.0 - - - +
538A GLY* 3.7 21.8 - - - -
541A LEU* 4.0 15.9 - - - +
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Residues in contact with CYS 92 (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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88A PHE* 2.9 49.1 + - - -
89A LYS* 3.0 13.6 + - + +
91A GLY* 1.3 75.3 - - - +
93A TYR* 1.3 60.0 + - - +
95A GLN* 2.9 21.1 + - - +
96A LYS* 3.0 19.8 + - + +
534A GLU 4.7 13.0 - - - +
538A GLY* 5.4 0.7 - - - +
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Residues in contact with TYR 93 (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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89A LYS* 3.0 15.9 + - + +
90A LEU* 4.2 11.4 - - + +
92A CYS* 1.3 76.1 - - - +
94A ILE* 1.3 63.9 + - + +
96A LYS* 3.8 6.1 + - + +
97A ASN* 2.9 51.5 + - - +
101A PHE* 4.0 24.3 - + - -
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Residues in contact with ILE 94 (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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90A LEU* 2.9 40.3 + - + +
91A GLY* 4.1 4.9 - - - +
93A TYR* 1.3 77.3 - - + +
95A GLN* 1.3 63.8 + - - +
97A ASN 3.2 18.7 + - - +
98A CYS* 3.9 3.8 + - - -
101A PHE* 3.6 33.4 - - + -
537A THR* 4.7 3.8 - - + -
541A LEU* 5.4 2.9 - - + -
589A LEU 6.0 0.9 - - - +
590A LEU* 4.6 24.0 - - + +
593A PRO* 4.0 37.7 - - + +
594A ALA* 4.3 8.2 - - + +
597A SER* 4.6 2.1 + - - -
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Residues in contact with GLN 95 (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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91A GLY 2.9 21.2 + - - +
92A CYS* 2.9 9.8 + - - +
94A ILE* 1.3 78.4 - - - +
96A LYS* 1.3 65.8 + - + +
97A ASN 3.3 1.0 + - - -
98A CYS* 4.0 4.3 + - - +
533A PHE* 4.8 16.2 + - - +
534A GLU* 4.4 15.7 - - - +
536A ARG* 5.0 5.5 - - - +
537A THR* 2.9 38.9 + - - +
538A GLY 5.6 0.2 - - - +
597A SER* 2.9 34.8 + - - +
600A LEU* 5.6 6.9 - - - +
601A TYR* 3.8 29.7 + - - +
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Residues in contact with LYS 96 (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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92A CYS 3.0 17.2 + - - +
93A TYR* 3.8 8.7 + - + +
94A ILE 3.3 0.6 - - - -
95A GLN* 1.3 79.9 - - + +
97A ASN* 1.3 70.1 + - - +
98A CYS* 3.6 4.0 + - - -
100A LYS* 4.8 5.7 - - - +
601A TYR* 5.2 9.3 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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