Contacts of the helix formed by residues 109 - 118 (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 ALA 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ALA* 4.9 10.3 - - + +
8A HIS* 4.5 14.3 - - + -
107A GLY 3.3 5.5 + - - +
108A PHE* 1.3 76.5 - - - +
110A GLU* 1.3 65.9 + - - +
111A TYR 3.2 1.2 + - - -
112A GLY* 3.3 5.8 + - - -
113A ARG* 3.3 24.8 + - + +
323A ARG* 6.1 0.9 - - - +
327A ASN* 6.2 0.2 - - - +
328A TYR* 5.0 4.6 - - + -
990A TPO 5.3 0.8 + - - +
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Residues in contact with GLU 110 (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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7A ALA* 5.5 0.7 - - - +
8A HIS* 2.6 32.7 + - - +
86A THR* 4.0 14.8 - - + -
89A ILE* 4.2 10.1 - - + -
90A PHE* 3.3 19.3 - - + -
108A PHE* 3.3 32.2 + - + -
109A ALA* 1.3 75.4 - - - +
111A TYR* 1.3 65.1 + - - +
113A ARG* 2.9 41.8 + - - +
114A ALA* 2.8 26.9 + - - +
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Residues in contact with TYR 111 (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* 3.8 35.2 - - + -
103A ILE* 4.2 23.8 - - + -
104A VAL 5.7 3.6 - - - -
107A GLY* 4.6 4.3 - - - -
108A PHE* 3.2 39.3 - + + +
109A ALA 3.2 1.2 + - - -
110A GLU* 1.3 76.8 - - - +
112A GLY* 1.3 58.8 + - - +
114A ALA* 3.8 1.6 - - - +
115A LEU* 3.0 36.5 + - + +
151A PHE* 4.6 30.5 - + + -
152A LEU 5.1 2.5 - - - -
153A CYS* 3.2 25.4 - - + +
185A ASP* 2.5 44.1 + - + +
211A LEU* 4.9 3.1 - - + -
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Residues in contact with GLY 112 (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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103A ILE* 4.6 15.8 - - - +
108A PHE 4.8 0.6 + - - -
109A ALA 3.3 7.3 + - - -
110A GLU 3.3 0.2 - - - -
111A TYR* 1.3 77.6 - - - +
113A ARG* 1.3 60.0 + - - +
115A LEU* 4.6 0.7 - - - -
116A ALA* 2.9 32.2 + - - +
122A ILE* 3.9 16.3 - - - +
124A ARG* 5.7 2.9 - - - -
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Residues in contact with ARG 113 (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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7A ALA* 6.1 4.5 - - - -
90A PHE* 3.6 18.3 - - + -
109A ALA* 3.3 17.0 + - + +
110A GLU* 2.9 46.0 + - - +
112A GLY* 1.3 77.3 - - - +
114A ALA* 1.3 62.1 + - - +
116A ALA* 3.8 4.3 - - - +
117A GLN* 3.2 47.7 + - - +
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Residues in contact with ALA 114 (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* 4.0 11.7 - - + -
90A PHE* 3.6 35.4 - - + -
93A ALA* 3.7 24.5 - - + +
110A GLU 2.8 16.6 + - - +
111A TYR 3.8 3.1 - - - +
113A ARG* 1.3 77.3 - - - +
115A LEU* 1.3 61.0 + - - +
117A GLN* 3.5 2.8 + - - +
118A SER* 3.1 22.3 + - - -
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Residues in contact with LEU 115 (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* 4.3 9.4 - - + -
98A PRO* 3.5 31.6 - - + -
101A ALA* 4.1 9.9 - - + -
103A ILE* 3.7 27.6 - - + -
111A TYR 3.0 22.8 + - - +
112A GLY 4.8 0.2 - - - +
114A ALA* 1.3 75.2 - - - +
116A ALA* 1.3 63.7 + - - +
118A SER* 2.9 20.6 + - - +
120A CYS* 3.2 22.5 + - + -
122A ILE* 3.7 24.5 - - + -
151A PHE* 3.8 30.1 - - + -
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Residues in contact with ALA 116 (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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112A GLY 2.9 18.8 + - - +
113A ARG* 3.8 5.6 - - - +
115A LEU* 1.3 76.5 - - - +
117A GLN* 1.3 65.8 + - + +
119A GLY* 3.0 14.4 + - - -
120A CYS 5.1 3.4 - - - +
122A ILE* 3.9 10.7 - - + +
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Residues in contact with GLN 117 (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* 3.4 28.0 - - + -
113A ARG* 3.2 41.4 + - - +
114A ALA 3.9 3.8 - - - +
116A ALA* 1.3 77.9 - - + +
118A SER* 1.3 58.7 + - - +
119A GLY 3.2 1.0 + - - -
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Residues in contact with SER 118 (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 4.2 22.3 + - - -
94A SER* 4.8 7.6 - - - -
97A LYS* 5.2 10.8 - - - +
98A PRO* 4.7 5.4 + - - +
114A ALA 3.1 11.0 + - - -
115A LEU* 2.9 25.1 + - - +
116A ALA 3.1 0.2 - - - -
117A GLN* 1.3 77.1 - - - +
119A GLY* 1.3 60.4 + - - +
120A CYS* 4.0 8.3 - - - +
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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
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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