Contacts of the helix formed by residues 78 - 101 (chain A) in PDB entry 5LEZ
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 MET 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA* 4.3 16.4 - - + +
75A TYR* 4.0 1.8 - - - -
77A GLY* 1.3 70.9 - - - -
79A GLY* 1.3 66.8 + - - +
80A PRO* 3.4 9.2 - - + -
81A ASP* 3.1 22.3 + - + +
82A TYR 3.2 9.4 + - - -
127A ARG* 3.9 27.8 - - - +
130A GLY* 3.0 31.5 + - - +
131A VAL* 3.2 6.7 - - - +
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Residues in contact with GLY 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 3.4 28.6 + - - -
77A GLY 3.5 5.9 + - - -
78A MET* 1.3 70.9 - - - +
80A PRO* 1.3 68.8 - - - +
82A TYR* 3.0 19.2 - - - +
83A ARG* 3.1 15.0 + - - +
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Residues in contact with PRO 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A MET* 3.4 10.1 - - + -
79A GLY* 1.3 90.5 - - - +
81A ASP* 1.3 63.6 + - - +
83A ARG* 3.4 43.0 + - - +
84A VAL* 3.5 15.3 + - - +
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Residues in contact with ASP 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A MET* 3.1 20.3 + - + +
80A PRO* 1.3 80.7 - - - +
82A TYR* 1.3 60.6 + - - +
84A VAL* 3.3 23.7 + - - +
85A LEU* 3.5 10.0 + - - +
127A ARG* 2.8 43.6 + - - -
129A PHE* 3.5 19.2 - - + -
130A GLY* 2.9 18.8 + - - +
131A VAL* 3.5 13.2 - - + -
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Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A HIS 4.7 3.4 - - - -
63A LYS* 2.6 31.9 + - - -
65A GLU* 3.7 14.7 - - + +
73A LEU* 2.9 44.1 + - + +
74A VAL* 3.9 4.7 - - - -
75A TYR* 3.3 53.2 - + + -
78A MET 3.2 5.4 + - - +
79A GLY* 3.0 15.9 - - - +
81A ASP* 1.3 77.2 - - - +
83A ARG* 1.3 62.1 + - + +
85A LEU* 3.0 6.8 + - - +
86A VAL* 2.9 41.5 + - + +
131A VAL* 3.6 7.4 - - + +
133A LEU* 3.6 11.4 - - + -
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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
----------------------------------------------------------
65A GLU* 6.0 1.8 - - - +
79A GLY 3.1 12.0 + - - +
80A PRO* 3.7 38.0 + - - +
81A ASP 3.3 0.8 - - - -
82A TYR* 1.3 81.1 - - + +
84A VAL* 1.3 65.1 + - - +
86A VAL* 3.4 9.1 + - + +
87A HIS* 3.1 24.6 + - - +
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PRO 3.5 13.7 + - - +
81A ASP* 3.3 12.7 + - - +
82A TYR 3.2 0.2 - - - -
83A ARG* 1.3 79.6 - - - +
85A LEU* 1.3 57.9 + - + +
87A HIS* 3.5 6.5 + - - +
88A ARG* 3.0 37.2 + - + +
120A TYR* 5.4 6.1 - - + +
129A PHE* 3.8 26.9 - - + -
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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
----------------------------------------------------------
73A LEU* 5.0 2.2 - - - -
81A ASP 3.5 6.7 + - - +
82A TYR* 3.0 7.2 + - - +
84A VAL* 1.3 75.2 - - + +
86A VAL* 1.3 58.7 + - - +
88A ARG* 3.9 5.2 - - + +
89A ALA* 2.8 36.5 + - - +
113A VAL* 4.4 12.7 - - + +
116A VAL* 4.4 13.0 - - + -
117A MET* 3.9 30.5 - - + -
129A PHE* 4.0 36.8 - - + -
131A VAL* 3.5 32.5 - - + -
133A LEU* 4.3 19.3 - - + -
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLU* 4.4 11.9 - - + +
67A ILE* 4.2 11.9 - - + -
73A LEU* 4.1 6.9 - - + +
82A TYR* 2.9 58.2 + - + +
83A ARG* 3.4 9.6 + - + +
85A LEU* 1.3 77.0 - - - +
87A HIS* 1.3 63.6 + - - +
89A ALA* 3.6 1.8 - - - +
90A ARG* 3.0 67.7 + - - +
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Residues in contact with HIS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ARG 3.1 17.1 + - - +
84A VAL* 3.6 6.3 - - - +
86A VAL* 1.3 77.9 - - - +
88A ARG* 1.3 74.7 + - + +
90A ARG* 3.3 12.0 + - - +
91A LYS* 3.1 33.5 + - + +
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Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 3.0 31.8 + - + +
85A LEU* 3.9 7.6 - - + +
86A VAL 3.4 0.2 - - - -
87A HIS* 1.3 79.8 - - + +
89A ALA* 1.3 62.2 + - - +
91A LYS* 3.1 19.2 + - - +
92A LEU* 2.8 58.4 + - + +
95A GLN* 4.9 2.6 + - - +
113A VAL* 5.9 1.3 - - + -
116A VAL* 3.7 40.7 - - + +
119A GLU* 5.6 1.6 + - - -
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Residues in contact with ALA 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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67A ILE* 3.9 23.3 - - + -
73A LEU* 5.2 5.8 - - + -
85A LEU 2.8 22.9 + - - +
86A VAL 3.6 4.3 - - - +
88A ARG* 1.3 71.8 - - - +
90A ARG* 1.3 57.8 + - - +
92A LEU* 3.4 2.6 + - - +
93A ALA* 2.9 24.9 + - - +
109A LEU* 3.4 14.9 - - + +
113A VAL* 3.7 28.2 - - + +
135A ILE* 6.3 0.2 - - + -
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLU* 3.4 26.1 + - - -
66A PRO* 2.9 33.1 + - - +
67A ILE* 3.8 29.3 + - + +
86A VAL* 3.0 42.8 + - - +
87A HIS* 3.6 9.5 - - - +
89A ALA* 1.3 76.8 - - - +
91A LYS* 1.3 61.8 + - - +
93A ALA* 3.3 4.3 + - - +
94A GLN* 3.1 28.0 + - + +
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Residues in contact with LYS 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 HIS* 3.1 27.7 + - + +
88A ARG* 3.1 19.7 + - - +
90A ARG* 1.3 75.3 - - - +
92A LEU* 1.3 58.1 + - - +
94A GLN* 3.4 7.9 + - + +
95A GLN* 3.0 61.9 + - - +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ARG* 2.8 46.7 + - + +
89A ALA 3.7 4.0 - - - +
91A LYS* 1.3 73.9 - - - +
93A ALA* 1.3 64.1 + - - +
95A GLN* 3.5 19.1 + - + +
96A TYR* 3.1 24.8 + - - +
104A ILE* 4.4 2.7 - - - +
109A LEU* 4.4 7.9 - - + -
112A ARG* 4.0 51.4 + - + +
113A VAL* 4.1 12.1 - - + -
116A VAL* 4.4 9.9 - - + -
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Residues in contact with ALA 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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67A ILE* 4.2 3.6 - - + +
68A THR* 3.5 33.4 - - + +
89A ALA 2.9 15.3 + - - +
90A ARG* 3.5 9.4 - - - +
92A LEU* 1.3 76.3 - - - +
94A GLN* 1.3 61.4 + - - +
96A TYR* 3.6 3.6 - - - +
97A TYR* 3.0 26.3 + - - +
104A ILE* 3.9 23.0 + - + +
109A LEU* 4.1 5.1 - - + +
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Residues in contact with GLN 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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67A ILE 5.4 3.2 + - - -
68A THR* 5.3 8.1 - - - +
90A ARG 3.1 19.3 + - - +
91A LYS* 3.8 9.4 - - + +
92A LEU 3.3 0.2 - - - -
93A ALA* 1.3 79.7 - - - +
95A GLN* 1.3 59.7 + - + +
97A TYR* 3.1 19.0 + - - +
98A LEU* 2.8 43.7 + - + +
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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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88A ARG* 4.9 2.9 + - - +
91A LYS* 3.0 52.7 + - - +
92A LEU* 3.7 28.6 - - + +
94A GLN* 1.3 75.4 - - - +
96A TYR* 1.3 63.6 + - - +
98A LEU* 3.3 17.8 + - + +
99A VAL* 3.4 19.7 + - - +
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Residues in contact with TYR 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 LEU 3.1 15.8 + - - +
93A ALA 3.6 4.7 - - - +
95A GLN* 1.3 79.6 - - - +
97A TYR* 1.3 57.5 + - - +
99A VAL* 3.3 3.1 + - - -
100A TYR* 3.0 64.0 + + + +
102A GLU* 3.6 29.0 + - + -
103A PRO 4.1 1.6 - - - -
104A ILE* 3.6 43.7 - - + -
105A PRO* 3.3 23.3 - - + +
108A GLN* 4.5 7.2 - - + +
112A ARG* 3.9 27.1 - - - +
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Residues in contact with TYR 97 (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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93A ALA 3.0 18.2 + - - +
94A GLN* 3.1 21.9 + - - +
96A TYR* 1.3 76.7 - - - +
98A LEU* 1.3 64.4 + - + +
101A GLN* 2.8 65.6 + - - +
102A GLU* 3.3 41.5 - - - +
103A PRO* 3.9 15.5 - - + -
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Residues in contact with LEU 98 (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 LYS* 6.3 1.6 - - - +
94A GLN* 2.8 30.7 + - + +
95A GLN* 3.8 11.0 - - + +
96A TYR 3.2 0.4 - - - -
97A TYR* 1.3 82.4 - - + +
99A VAL* 1.3 64.3 + - + +
101A GLN* 3.6 18.1 + - - +
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLN 3.5 14.4 - - - +
96A TYR* 3.3 5.8 + - - +
97A TYR 3.3 0.2 - - - -
98A LEU* 1.3 80.6 - - + +
100A TYR* 1.3 94.8 + - + +
101A GLN* 3.6 3.2 + - - +
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Residues in contact with TYR 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A TYR* 3.0 69.5 + + + +
99A VAL* 1.3 101.6 - - + +
101A GLN* 1.3 71.0 + - - +
102A GLU* 3.2 13.6 + - + +
112A ARG* 5.1 5.9 + - - -
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Residues in contact with GLN 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TYR* 2.8 67.1 + - + +
98A LEU* 3.6 22.8 + - - +
99A VAL 4.8 2.5 - - - +
100A TYR* 1.3 79.4 - - - +
102A GLU* 1.3 58.0 + - - +
103A PRO* 4.9 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
------------------------------------------------------------
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