Contacts of the helix formed by residues 83 - 98 (chain A) in PDB entry 3LKB
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 ALA 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ASP* 5.7 2.8 + - - +
58A TYR* 3.3 36.8 - - + -
60A ASN* 4.7 4.9 - - - +
63A THR* 5.9 0.2 - - - +
82A TYR* 1.3 80.0 - - + +
84A THR* 1.3 64.2 + - - +
85A GLY 4.2 1.3 - - - +
86A ALA* 3.8 21.3 - - + +
87A ASN* 2.8 29.0 + - - +
105A SER* 4.1 0.2 - - - -
393A VAL* 3.3 8.3 - - - -
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Residues in contact with THR 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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83A ALA* 1.3 68.5 - - - +
85A GLY* 1.3 64.6 + - - +
87A ASN* 3.8 2.7 - - - +
88A LEU* 2.9 36.3 + - + +
105A SER* 2.8 13.9 + - - -
107A HIS* 3.6 30.1 - - + +
110A LEU* 4.4 1.1 - - + +
126A TYR* 3.8 4.7 - - - -
154A PRO* 4.0 16.4 - - + +
155A PHE* 3.8 17.1 - - - -
393A VAL* 2.6 36.4 - - - +
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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
----------------------------------------------------------
58A TYR* 5.3 2.0 + - - -
60A ASN* 3.8 16.8 + - - -
83A ALA* 3.3 3.0 - - - +
84A THR* 1.3 78.6 - - - +
86A ALA* 1.3 61.6 + - - +
88A LEU* 3.5 5.9 + - - +
89A GLN* 3.2 22.7 + - - +
154A PRO* 4.0 25.7 - - - +
155A PHE 5.2 0.2 - - - +
393A VAL* 5.1 0.2 - - - +
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Residues in contact with ALA 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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56A ASP* 5.7 0.4 - - - +
60A ASN* 3.3 25.1 + - - +
63A THR* 3.9 33.2 - - + +
81A SER* 6.6 0.2 - - - -
82A TYR 6.1 0.2 - - - +
83A ALA* 3.4 19.1 + - + +
84A THR 3.2 0.4 - - - -
85A GLY* 1.3 74.5 - - - +
87A ASN* 1.3 60.3 + - - +
89A GLN* 3.1 5.8 + - - +
90A LEU* 2.9 36.4 + - + +
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Residues in contact with ASN 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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79A PHE* 5.1 1.0 - - - -
81A SER* 2.7 38.7 + - - -
82A TYR 3.6 10.4 + - - +
83A ALA 2.8 26.6 + - - +
84A THR 3.8 1.1 - - - +
86A ALA* 1.3 78.4 - - - +
88A LEU* 1.3 62.5 + - - +
89A GLN 3.3 0.2 + - - -
90A LEU* 3.3 7.2 + - - +
91A LYS* 3.0 27.5 + - + +
94A ILE* 4.7 7.7 - - - +
101A THR* 3.8 13.9 - - - +
103A PRO* 3.8 17.3 - - - +
105A SER* 4.4 0.3 - - - -
110A LEU* 3.7 23.5 - - + +
119A ILE* 5.4 4.0 - - + +
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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 THR* 2.9 37.9 + - + +
85A GLY* 3.7 5.4 - - - +
87A ASN* 1.3 76.4 - - - +
89A GLN* 1.3 61.4 + - - +
91A LYS* 3.4 26.3 + - + +
92A PRO* 4.0 4.0 - - - +
107A HIS* 4.3 10.3 - - + +
109A GLU* 3.9 25.1 - - + +
110A LEU* 3.8 18.6 - - + +
154A PRO* 4.5 11.9 - - + -
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Residues in contact with GLN 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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60A ASN* 3.6 40.8 - - - +
61A ALA* 5.5 0.5 - - - -
64A GLN* 4.0 17.7 - - - +
85A GLY 3.2 7.5 + - - +
86A ALA* 3.1 11.1 + - - +
88A LEU* 1.3 79.9 - - - +
90A LEU* 1.3 66.1 + - + +
92A PRO* 3.5 13.2 - - - +
93A LEU* 5.3 0.3 + - - +
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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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60A ASN 5.7 0.9 - - - +
63A THR* 4.1 22.0 - - + -
64A GLN* 4.1 34.8 - - + +
67A PHE* 4.5 17.5 - - + -
79A PHE* 3.9 26.5 - - + -
86A ALA* 2.9 18.9 + - - +
87A ASN* 3.3 4.2 + - - +
89A GLN* 1.3 80.3 - - + +
91A LYS* 1.3 53.6 + - - +
92A PRO* 3.3 2.2 - - - -
93A LEU* 3.0 14.5 + - + -
94A ILE* 2.8 46.5 + - + +
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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 ASN 3.0 20.3 + - - +
88A LEU* 3.7 22.9 - - + +
89A GLN 3.4 0.4 - - - -
90A LEU* 1.3 73.1 - - - +
92A PRO* 1.4 72.2 - - + +
94A ILE* 3.1 7.7 + - - +
95A GLN* 3.0 25.6 + - - +
109A GLU* 2.8 24.2 + - - -
110A LEU* 3.2 25.8 + - + +
112A ASP 2.7 27.6 + - - -
113A PRO 4.7 0.6 - - - -
114A PRO* 3.2 19.7 + - - +
115A ASN* 3.5 19.6 - - + +
119A ILE* 3.6 15.3 - - + -
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Residues in contact with PRO 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 4.0 4.5 - - - +
89A GLN 3.5 16.4 - - - +
90A LEU 3.6 0.7 - - - -
91A LYS* 1.4 94.3 - - + +
93A LEU* 1.3 55.9 + - + +
95A GLN* 3.6 2.6 - - - +
96A GLU* 3.0 28.3 + - - +
115A ASN* 3.6 26.0 - - - +
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Residues in contact with LEU 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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64A GLN* 5.1 4.7 - - + +
67A PHE* 4.0 23.6 - - + -
68A GLU* 4.3 23.1 - - + +
90A LEU* 3.0 20.7 + - + +
92A PRO* 1.3 77.8 - - - +
94A ILE* 1.3 66.4 + - - +
96A GLU* 3.2 22.1 + - - +
97A LEU* 3.0 49.5 + - + +
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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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67A PHE* 4.3 13.2 - - + -
79A PHE* 4.1 8.5 - - + -
87A ASN* 4.7 8.3 - - - +
90A LEU* 2.8 41.8 + - + +
91A LYS* 3.7 8.5 - - - +
93A LEU* 1.3 73.8 - - - +
95A GLN* 1.3 57.4 + - - +
97A LEU* 3.7 6.6 - - - -
98A ARG* 2.8 25.5 + - - -
99A ILE* 3.3 30.6 + - + +
101A THR* 3.4 32.3 - - + +
115A ASN 5.8 0.2 - - - +
118A TYR* 4.1 13.1 - - + -
119A ILE* 4.4 14.8 - - + -
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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 LYS 3.0 15.5 + - - +
92A PRO 3.6 2.2 - - - +
94A ILE* 1.3 77.9 - - - +
96A GLU* 1.3 63.9 + - - +
98A ARG* 3.2 19.6 + - - +
115A ASN* 3.1 43.4 + - + +
117A ASP* 2.9 52.1 + - - +
118A TYR* 3.8 20.6 + - - -
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Residues in contact with GLU 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 PRO 3.0 18.3 + - - +
93A LEU* 3.2 22.6 + - - +
95A GLN* 1.3 76.5 - - - +
97A LEU* 1.3 64.6 + - + +
98A ARG* 3.5 9.0 + - - +
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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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67A PHE* 4.3 15.0 - - + -
71A VAL* 4.1 28.3 - - + -
93A LEU* 3.0 44.2 + - + +
94A ILE 4.1 1.6 - - - +
96A GLU* 1.3 79.9 - - + +
98A ARG* 1.3 71.1 + - - +
99A ILE* 2.9 49.8 + - + +
313A ASN* 3.3 13.0 + - - -
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Residues in contact with ARG 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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94A ILE 2.8 11.4 + - - -
95A GLN* 3.2 10.9 + - - +
96A GLU 4.0 6.3 + - - +
97A LEU* 1.3 79.2 - - - +
99A ILE* 1.3 59.2 + - - +
100A PRO* 3.5 4.9 - - - +
118A TYR* 3.0 56.6 + - + +
313A ASN* 3.1 25.9 + - - +
314A GLU* 5.5 12.1 - - + +
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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