Contacts of the helix formed by residues 108 - 120 (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 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 4.3 18.4 - - - +
2A ILE* 3.7 20.4 - - - -
40A ASN* 5.7 3.1 - - - +
106B ASN 3.9 0.8 + - - -
107B PRO* 1.3 72.7 - - - +
109B LEU* 1.3 55.6 + - - +
110B GLN* 3.2 0.4 - - - -
111B LEU* 3.0 19.4 + - - +
112B ALA* 2.6 34.0 + - - +
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Residues in contact with LEU 109 (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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2A ILE* 3.6 8.9 - - + +
40A ASN* 3.3 25.4 - - + +
41A PRO* 3.6 24.5 - - + +
43A LEU* 3.6 36.7 - - + +
46A ALA* 3.7 13.7 - - + -
57A LEU* 5.7 1.3 - - + -
61A PHE* 3.3 49.1 - - + -
107B PRO 3.4 0.6 + - - +
108B SER* 1.3 71.4 - - - +
110B GLN* 1.3 64.7 + - - +
112B ALA* 3.0 6.7 + - - +
113B LEU* 2.9 26.7 + - + +
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Residues in contact with GLN 110 (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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1A MET* 4.1 5.4 - - - +
2A ILE* 3.4 19.9 - - + +
61A PHE* 5.2 2.2 - - + +
62A GLN 3.5 23.8 - - - +
63A TRP* 3.8 8.1 - - + -
64A GLN* 2.4 42.9 + - - +
66A GLU* 2.6 34.8 + - - -
108B SER* 3.2 0.6 - - - -
109B LEU* 1.3 79.4 - - - +
111B LEU* 1.3 65.4 + - - +
113B LEU* 3.0 27.9 + - + +
114B LYS* 3.0 28.4 + - - +
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Residues in contact with LEU 111 (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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66A GLU 4.0 17.5 - - - +
90B LEU* 3.8 39.0 - - + +
92B VAL* 4.3 15.0 - - + -
97B ILE* 4.7 6.3 - - + -
107B PRO* 4.7 2.9 - - + -
108B SER* 3.0 30.0 + - - +
110B GLN* 1.3 83.5 - - - +
112B ALA* 1.3 49.6 + - - +
114B LYS* 2.8 13.4 + - + +
115B ILE* 2.6 58.0 + - + -
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Residues in contact with ALA 112 (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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43A LEU* 3.3 32.5 - - + -
107B PRO* 4.3 5.4 - - + -
108B SER 2.6 15.6 + - - +
109B LEU 3.2 10.1 - - - +
111B LEU* 1.3 73.5 - - - +
113B LEU* 1.3 62.9 + - + +
115B ILE* 3.0 13.9 + - - +
116B ALA 3.0 19.2 + - - -
123B LEU* 3.2 19.8 - - + +
127B PHE* 4.0 6.1 - - + -
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Residues in contact with LEU 113 (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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57A LEU* 3.3 22.7 - - + -
58A GLU* 3.2 29.2 - - - +
61A PHE* 4.0 15.9 - - + +
63A TRP* 3.1 42.0 - - + +
109B LEU* 2.9 16.2 + - + +
110B GLN* 3.0 21.1 + - + +
112B ALA* 1.3 76.3 - - + +
114B LYS* 1.3 52.1 - - - +
116B ALA* 3.4 3.3 + - - +
117B TYR* 2.8 35.0 + - - +
123B LEU* 4.3 18.8 - - + -
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A TRP* 3.3 35.9 - - + -
64A GLN 2.4 24.5 + - - -
65A PRO* 2.9 13.9 + - - +
66A GLU 2.4 33.9 + - - +
90B LEU* 3.3 24.2 - - + +
110B GLN* 3.1 27.4 - - - +
111B LEU* 2.8 18.3 + - + +
113B LEU* 1.3 75.1 - - - +
115B ILE* 1.3 53.7 + - - +
117B TYR* 3.4 1.7 - - + +
118B TYR* 2.7 42.2 + - + +
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Residues in contact with ILE 115 (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* 4.7 20.0 - - + -
86B LEU* 5.2 7.7 - - + +
90B LEU* 3.4 22.4 - - + -
97B ILE* 4.6 9.6 - - + -
100B ILE* 5.3 1.3 - - + -
107B PRO* 3.7 27.6 - - + -
111B LEU* 2.6 41.2 + - + +
112B ALA* 3.3 13.0 - - - +
114B LYS* 1.3 72.7 - - - +
116B ALA* 1.3 54.1 + - - +
118B TYR* 4.0 0.7 - - - +
119B LEU* 2.7 40.5 + - + +
126B ILE* 4.0 16.4 - - + -
127B PHE* 4.4 7.2 - - + -
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Residues in contact with ALA 116 (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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112B ALA 3.0 5.1 + - - -
113B LEU 3.7 3.4 - - - +
115B ILE* 1.3 76.6 - - - +
117B TYR* 1.3 54.3 + - - +
119B LEU* 4.1 4.0 - - - -
120B ASN* 2.5 30.3 + - - -
121B THR 2.8 30.8 + - - +
122B PRO* 4.2 1.1 - - + -
123B LEU* 3.3 39.5 - - + +
126B ILE* 4.2 4.9 - - + -
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Residues in contact with TYR 117 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A TRP* 3.7 30.5 - + + -
113B LEU 2.8 18.9 + - - +
114B LYS* 3.1 4.0 + - - +
116B ALA* 1.3 76.4 - - - +
118B TYR* 1.3 92.4 + + - +
120B ASN* 2.8 32.5 + - - +
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Residues in contact with TYR 118 (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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86B LEU* 4.7 8.5 - - + -
89B LEU* 3.0 77.1 + - + +
90B LEU* 4.0 9.2 - - + -
114B LYS* 2.7 32.3 + - + +
115B ILE 4.2 0.9 - - - +
117B TYR* 1.3 96.3 - + - +
119B LEU* 1.3 65.4 + - - +
120B ASN* 3.1 7.3 + - - +
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Residues in contact with LEU 119 (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* 4.1 17.7 - - + -
75B ILE* 3.0 36.1 - - + -
76B ARG* 4.8 2.0 - - + -
79B LYS* 2.4 36.4 + - - +
81B ILE* 3.8 38.5 - - + +
86B LEU* 4.9 12.4 - - + +
115B ILE* 2.7 30.4 + - + +
116B ALA* 3.9 4.7 - - - +
118B TYR* 1.3 75.1 - - - +
120B ASN* 1.3 56.7 + - - +
121B THR* 3.1 19.1 - - - +
126B ILE* 4.7 2.5 - - + -
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Residues in contact with ASN 120 (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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79B LYS* 2.9 6.7 + - - +
116B ALA 2.5 13.6 + - - -
117B TYR* 2.8 27.5 + - - +
118B TYR 3.1 5.9 + - - +
119B LEU* 1.3 74.6 - - - +
121B THR* 1.3 68.8 + - - +
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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