Contacts of the helix formed by residues 96 - 108 (chain B) in PDB entry 1L1E
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 SER 96 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ASP* 4.4 18.1 + - - +
75B TRP* 5.7 0.3 - - - -
94B THR* 3.1 5.0 + - - +
95B LEU* 1.3 77.1 - - - +
97B GLU* 1.3 63.9 + - - +
98B ASN* 3.3 10.4 + - - +
99B GLN* 3.2 43.8 + - - +
100B ALA* 3.0 21.5 + - - +
120B LEU* 4.1 2.0 - - - -
901B SAH 3.9 3.5 + - - -
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ASP* 4.9 3.0 + - - -
95B LEU 3.8 2.7 + - - +
96B SER* 1.3 72.7 + - - +
98B ASN* 1.3 61.1 + - - +
100B ALA* 3.5 5.2 + - - +
101B GLY* 3.2 18.5 + - - -
120B LEU* 3.5 36.2 - - + +
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Residues in contact with ASN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ASP* 5.9 3.6 + - + -
18B LEU 5.6 4.6 + - - +
20B ASP* 3.6 29.2 + - - +
75B TRP* 2.9 36.2 - - - +
96B SER* 3.1 7.9 + - - +
97B GLU* 1.3 77.2 - - - +
99B GLN* 1.3 60.9 + - - +
101B GLY* 3.3 2.5 + - - -
102B HIS* 2.9 29.6 + - - +
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Residues in contact with GLN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B TYR* 5.8 0.7 - - - -
74B GLY* 3.2 29.5 - - - +
75B TRP* 3.3 52.1 - - + +
94B THR* 2.7 32.5 + - + +
96B SER* 3.2 24.5 + - - +
98B ASN* 1.3 73.3 - - - +
100B ALA* 1.3 57.4 + - - +
102B HIS 3.1 0.2 + - - -
103B VAL* 2.7 40.9 + - - +
901B SAH 2.8 24.6 + - - -
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Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B THR* 4.1 9.9 - - + +
96B SER 3.0 12.9 + - - +
97B GLU* 3.6 13.0 - - - +
99B GLN* 1.3 75.8 - - - +
101B GLY* 1.3 57.5 + - - +
103B VAL* 3.9 1.7 - - - +
104B GLN* 2.9 29.4 + - - +
118B VAL* 4.1 23.6 - - + +
120B LEU* 4.8 16.8 - - + +
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Residues in contact with GLY 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLU 3.2 11.3 + - - -
98B ASN* 3.8 2.5 - - - -
100B ALA* 1.3 77.2 - - - +
102B HIS* 1.3 64.6 + - - +
104B GLN* 3.4 6.8 - - - +
105B LYS* 3.1 25.3 + - - +
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Residues in contact with HIS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ASP* 4.7 4.9 - - - -
30B THR 5.9 1.3 - - - -
31B GLN* 3.6 23.3 + - + -
75B TRP* 3.5 46.6 + + + +
98B ASN* 2.9 20.6 + - - +
99B GLN 3.1 3.3 + - - +
101B GLY* 1.3 74.2 - - - +
103B VAL* 1.3 65.4 + - - +
105B LYS* 3.4 32.3 + - - +
106B MET* 3.1 36.1 + - + +
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B CYS* 4.5 6.5 - - - -
74B GLY 3.5 9.0 - - - +
75B TRP 3.4 7.0 - - - -
76B GLY* 3.3 31.6 - - - +
79B MET* 3.8 9.4 - - + -
99B GLN 2.7 24.6 + - - +
100B ALA 3.9 0.4 - - - +
102B HIS* 1.3 71.3 - - - +
104B GLN* 1.3 66.3 + - - +
106B MET* 3.3 8.7 + - - +
107B PHE* 2.9 43.4 + - + -
118B VAL* 3.1 29.4 - - + -
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Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ALA 2.9 19.7 + - - +
101B GLY* 3.4 9.9 - - - +
103B VAL* 1.3 75.5 - - - +
105B LYS* 1.3 59.8 + - - +
107B PHE* 2.9 33.3 + - - +
108B ASP* 3.1 26.1 + - - +
116B ARG 5.0 3.5 - - - +
117B ARG* 5.6 0.7 - - - -
118B VAL* 4.2 15.9 + - + +
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Residues in contact with LYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B GLY 3.1 10.6 + - - +
102B HIS* 3.4 45.0 + - - +
104B GLN* 1.3 80.2 - - - +
106B MET* 1.3 68.8 + - - +
108B ASP* 3.2 21.2 + - - +
109B GLN* 3.6 25.1 + - - +
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Residues in contact with MET 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B THR* 5.6 4.0 - - - +
75B TRP 3.6 24.5 - - - +
76B GLY* 4.3 8.1 - - - +
77B ALA* 4.3 9.2 - - + +
80B ARG* 3.7 56.3 - - - +
102B HIS* 3.1 29.0 + - + +
103B VAL* 3.4 7.4 - - - +
104B GLN 3.1 0.6 - - - -
105B LYS* 1.3 88.9 - - + +
107B PHE* 1.3 70.8 + - + +
109B GLN* 3.4 13.2 + - - +
110B MET* 3.5 14.9 + - + +
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Residues in contact with PHE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B GLY 5.4 0.4 - - - -
79B MET* 4.0 17.0 - - + -
80B ARG 4.9 4.3 - - - -
83B ILE* 4.4 6.5 - - + -
90B VAL* 3.7 19.1 - - + -
103B VAL* 2.9 38.1 + - + -
104B GLN* 2.9 17.6 + - - +
106B MET* 1.3 82.8 - - + +
108B ASP* 1.3 56.5 + - - +
109B GLN 3.1 10.6 + - - -
110B MET* 3.3 26.8 + - - +
116B ARG* 3.0 77.8 + - + +
117B ARG* 3.8 5.6 - - - -
118B VAL* 3.8 12.6 - - + -
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Residues in contact with ASP 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLN* 3.1 33.7 + - - +
105B LYS* 3.2 12.5 + - - +
107B PHE* 1.3 75.8 - - - +
109B GLN* 1.3 62.6 + - + +
110B MET 3.6 1.6 - - - +
116B ARG* 4.9 5.8 + - - +
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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