Contacts of the helix formed by residues 85 - 96 (chain A) in PDB entry 1LC7
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 GLU 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLY* 1.3 68.1 - - - -
86A THR* 1.3 66.4 + - - +
87A GLU 3.2 0.2 - - - -
88A SER* 3.0 12.3 + - - -
89A ILE* 3.0 28.0 + - + +
185A ASP* 2.5 36.9 - - - +
187A ALA* 3.2 24.8 - - - +
211A LEU* 3.6 22.6 - - + +
212A ARG* 3.1 37.6 - - - +
213A SER* 3.3 2.6 + - - -
226A GLY* 3.8 5.0 - - - -
800A PO4 2.9 22.8 + - - +
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Residues in contact with THR 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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83A ASN 5.1 0.9 - - - -
84A GLY 3.0 0.2 - - - -
85A GLU* 1.3 77.8 - - - +
87A GLU* 1.3 61.9 + - - +
89A ILE* 3.2 19.0 + - - +
90A PHE* 3.2 28.6 + - + -
108A PHE* 4.4 12.2 - - - -
110A GLU* 4.0 27.4 - - + -
224A ARG* 3.8 11.8 + - - -
800A PO4 2.9 18.3 + - - -
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Residues in contact with GLU 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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82A GLY* 3.3 7.6 - - - -
83A ASN* 2.7 43.5 + - + +
84A GLY 3.0 11.3 + - - +
86A THR* 1.3 79.1 - - - +
88A SER* 1.3 57.1 + - - +
90A PHE* 3.1 9.2 + - + +
91A THR* 2.8 42.0 + - - +
244A MET* 4.6 11.3 + - - +
247A SER* 2.9 33.1 + - - -
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Residues in contact with SER 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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80A LEU 4.7 1.0 + - - -
82A GLY* 4.3 7.5 - - - -
84A GLY 3.5 8.4 + - - -
85A GLU* 3.0 13.6 + - - -
87A GLU* 1.3 77.8 - - - +
89A ILE* 1.3 57.2 + - - +
91A THR* 3.3 9.2 + - - -
92A VAL* 2.9 31.2 + - - +
211A LEU* 3.7 21.5 - - - +
226A GLY 4.0 1.2 - - - -
227A TYR* 3.7 31.6 + - - -
228A LEU* 4.4 6.2 - - - +
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Residues in contact with ILE 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 GLU* 3.0 22.6 + - - +
86A THR* 3.4 10.8 - - - +
87A GLU 3.2 0.4 - - - -
88A SER* 1.3 74.5 - - - +
90A PHE* 1.3 66.1 + - + +
92A VAL* 3.1 12.3 - - + +
93A ALA* 3.0 23.1 + - + +
108A PHE* 3.7 36.6 - - + -
110A GLU* 4.0 25.4 - - + +
111A TYR* 3.8 24.7 - - + -
114A ALA* 4.0 8.5 - - + -
151A PHE* 5.6 3.6 - - + -
185A ASP* 4.4 5.2 - - - +
211A LEU* 3.8 20.9 - - + -
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Residues in contact with PHE 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 THR* 3.2 32.0 + - + +
87A GLU* 3.1 12.6 + - + +
89A ILE* 1.3 80.2 - - + +
91A THR* 1.3 58.4 + - - +
93A ALA* 3.8 0.3 - - - +
94A SER* 2.8 34.7 + - - -
110A GLU* 3.3 31.2 - - + -
113A ARG* 3.6 14.8 - - + -
114A ALA* 3.6 37.5 - - + -
117A GLN* 3.4 30.3 - - + -
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Residues in contact with THR 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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80A LEU* 4.1 24.0 - - + -
87A GLU* 2.8 34.7 + - - +
88A SER* 3.6 9.8 - - - -
89A ILE 3.2 0.4 - - - -
90A PHE* 1.3 73.9 - - - +
92A VAL* 1.3 58.6 + - - +
94A SER* 3.4 6.5 + - - +
95A GLY 2.8 24.4 + - - -
239A MET* 3.3 27.3 - - + +
243A GLN* 5.7 5.9 - - + +
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Residues in contact with VAL 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 SER 2.9 15.8 + - - +
89A ILE* 3.1 16.6 - - - +
91A THR* 1.3 73.6 - - - +
93A ALA* 1.3 64.5 + - - +
96A LEU* 2.8 59.1 + - + +
151A PHE* 3.9 23.1 - - + -
183A ILE* 4.2 17.0 - - + -
209A TRP* 4.1 28.0 - - + -
211A LEU* 4.8 7.0 - - + -
239A MET* 4.0 7.4 - - + -
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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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89A ILE* 3.0 18.4 + - + +
90A PHE 3.8 1.8 - - - +
92A VAL* 1.3 80.4 - - + +
94A SER* 1.3 58.1 + - - +
96A LEU* 5.1 0.2 - - - -
97A LYS* 3.0 27.9 + - - -
98A PRO* 3.6 9.9 - - - +
114A ALA* 3.7 34.1 - - + +
115A LEU* 4.3 15.3 - - + -
118A SER* 4.2 6.9 - - - +
151A PHE* 4.9 5.8 - - + -
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Residues in contact with SER 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 PHE 2.8 21.8 + - - -
91A THR* 3.4 8.8 + - - +
93A ALA* 1.3 74.9 - - - +
95A GLY* 1.3 64.4 + - - +
96A LEU 3.6 0.2 + - - -
97A LYS* 3.7 13.5 + - - +
118A SER* 4.8 10.1 - - - -
242A GLN* 4.3 8.1 + - - +
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Residues in contact with GLY 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 THR 2.8 22.6 + - - -
94A SER* 1.3 77.2 + - - +
96A LEU* 1.3 58.4 + - - +
97A LYS* 5.0 0.9 - - - +
238A ARG* 3.1 28.8 + - - -
239A MET* 3.6 20.0 - - - -
242A GLN* 3.9 15.7 - - - +
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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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92A VAL* 2.8 36.2 + - + +
93A ALA* 5.1 0.2 - - - -
95A GLY* 1.3 77.7 - - - +
97A LYS* 1.3 72.2 + - - +
98A PRO* 3.2 11.5 - - + +
149A CYS* 3.6 24.9 - - - -
151A PHE* 5.6 0.7 - - + -
181A ASN* 4.1 18.6 - - + +
183A ILE* 4.4 4.5 - - + -
209A TRP* 3.7 39.5 - - + +
235A ALA* 5.4 0.2 - - + -
238A ARG* 4.0 15.9 + - - +
239A MET* 3.8 9.2 - - + -
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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
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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