Contacts of the helix formed by residues 93 - 103 (chain B) in PDB entry 2LYL
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 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B ALA* 3.9 0.9 - - - -
92B VAL* 1.3 77.7 - - - +
94B ARG* 1.3 59.5 + - - +
95B GLN* 3.9 15.7 - - - -
96B THR* 2.4 32.2 + - - +
97B ILE* 2.9 15.6 + - - +
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Residues in contact with ARG 94 (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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83B GLN* 3.6 27.1 - - + -
84B SER* 2.3 55.9 + - - +
87B ALA* 3.8 10.1 - - - +
92B VAL 3.7 1.6 + - - -
93B SER* 1.3 70.1 - - - +
95B GLN* 1.3 56.8 + - - +
97B ILE* 2.8 2.0 + - - +
98B ASN* 2.4 50.9 + - + +
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Residues in contact with GLN 95 (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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93B SER* 4.2 11.2 - - - -
94B ARG* 1.3 76.1 - - - +
96B THR* 1.3 63.3 + - + +
98B ASN* 2.8 12.6 + - - +
99B GLY* 2.6 31.7 + - - -
104B LYS* 2.4 40.5 + - - +
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Residues in contact with THR 96 (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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92B VAL* 4.4 6.4 - - + +
93B SER* 2.4 38.7 + - - +
95B GLN* 1.3 87.8 - - + +
97B ILE* 1.3 53.7 + - - -
99B GLY* 3.3 1.0 - - - -
100B ILE* 2.7 45.6 + - + +
104B LYS* 4.1 1.6 - - - +
105B TYR* 3.0 40.2 - - + +
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Residues in contact with ILE 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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72B LEU* 4.8 15.9 - - + +
83B GLN* 4.3 9.0 - - - +
86B LEU* 3.5 24.0 - - + -
87B ALA* 3.5 15.5 - - + -
90B LEU* 3.5 15.3 - - + -
92B VAL* 3.3 34.5 - - + -
93B SER 2.9 13.2 + - - +
94B ARG* 2.8 6.4 + - - +
96B THR* 1.3 74.0 - - - +
98B ASN* 1.3 63.4 + - - +
99B GLY 3.3 0.2 + - - -
100B ILE* 3.4 27.3 + - + +
101B GLU* 3.5 12.3 + - - +
111B LEU* 4.7 2.9 - - + -
115B ILE* 4.6 10.8 - - + -
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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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83B GLN* 3.9 16.8 - - + +
94B ARG* 2.4 54.3 + - + +
95B GLN* 2.8 27.5 + - - +
97B ILE* 1.3 72.7 - - - +
99B GLY* 1.3 57.5 + - - +
101B GLU* 2.8 16.7 - - - +
102B LYS* 2.4 56.8 + - - +
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Residues in contact with GLY 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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95B GLN* 2.6 24.6 + - - -
96B THR 3.0 1.3 + - - -
98B ASN* 1.3 80.5 - - - +
100B ILE* 1.3 51.3 + - - +
102B LYS* 3.0 7.8 + - - +
103B ASN* 2.6 17.5 + - - -
104B LYS* 2.5 40.1 + - - -
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Residues in contact with ILE 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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70B ASN* 3.0 40.1 + - + +
72B LEU* 6.5 0.7 - - + -
96B THR* 2.7 27.8 + - - +
97B ILE* 3.6 23.8 - - + +
99B GLY* 1.3 70.9 - - - +
101B GLU* 1.3 66.3 + - - +
103B ASN* 3.3 12.1 + - - -
104B LYS* 3.5 17.3 + - + +
105B TYR* 3.2 23.3 - - + +
107B PRO* 3.6 40.6 - - + -
115B ILE* 5.3 1.1 - - + -
127B PHE* 5.0 1.8 - - + -
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Residues in contact with GLU 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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69B ILE 4.3 5.5 - - - +
70B ASN* 3.4 23.9 - - - +
72B LEU* 3.7 7.8 - - + +
73B LYS* 2.4 63.9 + - + +
83B GLN* 2.5 39.4 + - - +
97B ILE 3.5 3.8 + - - +
98B ASN* 2.8 25.4 - - - +
100B ILE* 1.3 81.1 - - - +
102B LYS* 1.3 86.0 + - - +
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Residues in contact with LYS 102 (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 LYS* 4.0 9.9 + - - +
83B GLN* 4.3 2.2 + - - -
98B ASN* 2.4 49.4 + - - +
99B GLY* 3.0 11.0 + - - +
101B GLU* 1.3 113.5 + - - +
103B ASN* 1.3 74.4 + - - +
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Residues in contact with ASN 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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99B GLY* 2.6 10.9 + - - -
100B ILE 3.3 6.3 + - - -
102B LYS* 1.3 85.1 - - - +
104B LYS* 1.3 72.7 + - - +
105B TYR* 3.6 1.0 + - - -
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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