Contacts of the helix formed by residues 77 - 97 (chain A) in PDB entry 2LOP
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 ILE 77 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LYS* 1.3 79.1 - - - +
78A MET* 1.3 59.6 + - - +
79A PRO* 3.4 4.3 - - - -
80A ALA* 4.0 15.9 - - + -
81A GLY* 2.6 47.7 + - - +
84A ALA* 5.9 2.9 - - + -
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Residues in contact with MET 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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67A MET* 4.7 22.7 - - + +
76A LYS* 4.2 17.2 - - + +
77A ILE* 1.3 80.7 - - - +
79A PRO* 1.4 71.8 - - + +
81A GLY* 4.2 0.2 - - - -
82A LEU* 3.6 15.9 + - - +
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Residues in contact with PRO 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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67A MET* 4.2 24.2 - - + -
69A VAL* 5.5 0.7 - - + +
70A ARG 5.5 0.2 - - - +
71A PHE* 4.6 9.6 - - - +
72A LYS 4.1 31.6 - - - +
74A SER* 5.5 3.6 - - - +
75A LYS 4.6 11.2 - - - +
76A LYS* 5.1 1.3 - - + +
77A ILE* 3.4 5.6 - - - +
78A MET* 1.4 96.8 - - + +
80A ALA* 1.3 72.9 + - + +
82A LEU* 3.0 22.5 + - + +
83A VAL* 3.5 6.4 + - - +
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Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 4.6 15.8 - - + -
73A ARG* 6.5 1.1 - - - -
74A SER 6.1 0.9 - - - +
76A LYS 5.1 2.5 - - - +
77A ILE* 4.0 23.1 - - + +
79A PRO* 1.3 81.5 - - + +
81A GLY* 1.3 56.1 + - - +
83A VAL* 2.6 35.1 + - - +
84A ALA* 2.9 10.1 + - - +
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Residues in contact with GLY 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 2.6 37.3 + - - +
78A MET 4.2 0.7 - - - -
80A ALA* 1.3 72.5 - - - +
82A LEU* 1.3 54.1 + - - +
84A ALA* 2.6 31.0 + - - +
85A GLY* 2.8 10.6 + - - -
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Residues in contact with LEU 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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60A ALA* 4.1 34.8 - - + +
63A LEU* 3.7 36.3 - - + -
64A ALA* 4.6 8.7 - - + +
67A MET* 4.4 22.4 - - - -
78A MET 3.6 10.8 + - - +
79A PRO* 3.0 13.7 + - + +
80A ALA 3.0 0.2 + - - -
81A GLY* 1.3 74.4 - - - +
83A VAL* 1.3 59.6 + - + +
85A GLY* 2.8 20.8 + - - +
86A LEU* 3.0 12.5 + - + +
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 3.8 41.1 - - + -
79A PRO 4.1 4.3 - - - +
80A ALA* 2.6 17.5 + - - +
82A LEU* 1.3 75.5 - - + +
84A ALA* 1.3 55.1 + - - +
86A LEU* 4.0 6.3 - - - +
87A SER* 3.0 32.4 + - - +
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Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 5.9 3.4 - - + -
80A ALA 2.9 6.9 + - - +
81A GLY* 2.6 26.5 + - - +
83A VAL* 1.3 74.3 - - - +
85A GLY* 1.3 53.9 - - - -
87A SER* 3.8 4.2 - - - -
88A LEU* 3.0 40.3 + - + +
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Residues in contact with GLY 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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29A LEU* 6.5 1.1 - - - -
81A GLY 2.8 7.5 + - - -
82A LEU* 2.8 9.0 + - - -
84A ALA* 1.3 76.4 - - - +
86A LEU* 1.3 64.1 - - - -
88A LEU* 3.2 6.6 + - - +
89A MET* 2.9 33.0 + - - +
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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
----------------------------------------------------------
56A SER* 3.7 42.8 - - - +
57A LEU* 4.4 4.7 - - + +
59A THR* 5.9 0.2 - - - -
60A ALA* 3.9 22.2 - - + +
82A LEU* 3.0 14.2 + - + +
83A VAL* 4.1 6.7 - - - +
85A GLY* 1.3 74.6 - - - +
87A SER* 1.3 67.6 + - - +
89A MET* 3.0 9.2 - - + +
90A MET* 3.0 35.7 + - + -
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL* 3.0 23.2 + - - +
84A ALA* 3.8 6.7 - - - -
86A LEU* 1.3 78.7 - - - +
88A LEU* 1.3 69.8 + - - +
90A MET* 2.9 19.4 + - - +
91A ILE* 3.0 26.5 + - - +
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Residues in contact with LEU 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 ALA* 3.0 29.0 + - + +
85A GLY* 3.2 6.9 + - - +
87A SER* 1.3 78.0 - - - +
89A MET* 1.3 70.4 + - + +
91A ILE* 3.5 19.3 + - + +
92A LEU* 3.0 38.8 + - + +
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Residues in contact with MET 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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32A GLY 5.9 2.2 - - - +
36A GLY* 5.7 9.4 - - - -
56A SER* 3.9 25.4 - - - +
85A GLY* 2.9 22.6 + - - +
86A LEU* 3.0 15.3 - - + +
87A SER 3.0 0.2 - - - -
88A LEU* 1.3 83.1 - - + +
90A MET* 1.3 68.0 + - - +
92A LEU* 3.0 20.2 + - + +
93A ARG* 2.8 21.9 + - - +
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Residues in contact with MET 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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53A VAL* 6.3 0.2 - - + -
86A LEU* 3.0 26.9 + - + +
87A SER* 2.9 12.0 + - - +
89A MET* 1.3 75.9 - - - +
91A ILE* 1.3 54.1 + - + +
93A ARG* 2.7 50.9 + - - +
94A LEU* 2.8 17.9 + - - +
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Residues in contact with ILE 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 SER* 3.0 32.3 + - - +
88A LEU* 3.7 21.1 - - + +
90A MET* 1.3 75.4 - - + +
92A LEU* 1.3 62.7 - - + +
94A LEU* 2.7 41.6 + - + +
95A VAL* 3.3 11.0 + - + +
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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
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88A LEU* 3.0 30.2 + - + +
89A MET* 3.0 22.0 + - + +
91A ILE* 1.3 81.5 - - + +
93A ARG* 1.3 57.7 + - - +
95A VAL* 3.4 6.4 + - - +
96A LEU* 2.8 31.9 + - + +
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Residues in contact with ARG 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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52A ASP* 6.3 0.4 - - + -
53A VAL* 3.6 50.0 - - + +
89A MET 2.8 11.0 + - - +
90A MET* 2.7 39.4 + - - +
92A LEU* 1.3 76.3 - - - +
94A LEU* 1.3 70.0 + - - +
95A VAL 3.0 2.2 - - - -
96A LEU* 3.7 15.9 - - + -
97A LEU* 2.9 48.4 + - - +
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Residues in contact with LEU 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 MET 2.8 8.2 + - - +
91A ILE* 2.7 25.4 + - + +
93A ARG* 1.3 86.9 - - - +
95A VAL* 1.3 60.6 + - + +
97A LEU* 3.8 13.9 - - + +
98A LEU* 4.5 1.9 + - - +
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Residues in contact with VAL 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 ILE* 3.3 13.7 + - + +
92A LEU* 3.9 7.0 - - - +
93A ARG 3.0 0.4 - - - -
94A LEU* 1.3 81.0 - - + +
96A LEU* 1.3 66.7 + - - +
97A LEU 3.0 1.8 - - - -
98A LEU* 2.8 22.2 + - + +
99A LEU* 3.1 12.8 + - + +
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Residues in contact with LEU 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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44A TYR* 6.0 6.5 - - + -
92A LEU* 2.8 22.1 + - + +
93A ARG* 3.1 19.7 + - + +
95A VAL* 1.3 77.0 - - - +
97A LEU* 1.3 66.1 + - - +
99A LEU* 2.8 43.7 + - + -
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Residues in contact with LEU 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 ARG* 2.9 43.1 + - - +
94A LEU* 3.8 12.6 - - + +
96A LEU* 1.3 77.1 - - - +
98A LEU* 1.3 65.1 + - - +
99A LEU 4.3 1.7 - - - -
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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