Contacts of the strand formed by residues 85 - 91 (chain B) in PDB entry 4LGD
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 TYR 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LYS* 5.2 4.9 - - - +
71B ILE* 3.6 27.2 - - + +
74B MET* 4.2 26.9 + - + -
75B GLN* 3.1 58.8 + - + +
77B CYS 5.8 0.2 + - - -
83B VAL 3.9 1.2 + - - -
84B LYS* 1.3 74.2 - - - +
86B TYR* 1.3 63.8 + - - +
87B GLY* 2.9 27.4 - - - -
88B SER* 2.9 34.3 + - - -
97B ILE* 3.5 26.7 - - + -
98B VAL 3.4 11.7 - - - -
99B MET* 4.6 4.7 - - + +
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Residues in contact with TYR 86 (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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10B LYS* 5.6 1.0 - - - +
11B LEU* 3.0 43.9 + - + +
12B LYS* 4.2 15.9 - - - -
13B LYS* 3.9 10.0 - - - +
14B LEU* 3.4 42.1 + - + +
19B LEU* 5.2 2.1 - - - +
51B GLN* 6.0 0.5 - - - +
52B VAL 5.6 0.3 + - - -
53B VAL* 3.6 19.4 - - + +
75B GLN* 4.7 4.6 + - - -
84B LYS* 4.4 17.6 - - + +
85B TYR* 1.3 79.5 - - - +
87B GLY* 1.3 59.2 + - - +
98B VAL* 3.0 23.2 + - + +
99B MET 3.2 31.9 - - - -
100B GLU* 3.6 25.0 - - + +
101B TYR 4.8 0.5 + - - -
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Residues in contact with GLY 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 4.3 2.0 - - - +
19B LEU* 4.2 17.3 - - - -
75B GLN* 4.8 2.9 - - - -
85B TYR* 2.9 30.9 - - - -
86B TYR* 1.3 81.4 - - - +
88B SER* 1.3 58.4 + - - -
98B VAL* 3.0 24.4 + - - +
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Residues in contact with SER 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 3.8 15.8 - - - +
71B ILE* 5.0 3.9 - - - +
85B TYR* 2.9 23.4 + - - -
87B GLY* 1.3 72.1 - - - -
89B TYR* 1.3 68.1 + - - +
95B LEU* 4.5 17.7 - - - +
96B TRP 2.9 18.4 - - - -
97B ILE* 4.4 4.0 - - - -
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Residues in contact with TYR 89 (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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14B LEU* 4.0 10.0 - - + +
18B SER* 2.6 25.1 + - - -
19B LEU* 3.2 37.9 - - + +
21B LYS 3.1 27.8 - - - -
23B PRO* 4.0 39.3 - - + -
26B VAL* 3.9 9.4 - - + +
27B PHE* 3.9 25.4 - + - -
88B SER* 1.3 77.4 - - - +
90B PHE* 1.3 59.5 + - - +
95B LEU* 3.5 9.2 - - - +
96B TRP* 2.7 39.8 + + + +
98B VAL* 4.3 14.8 - - + -
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Residues in contact with PHE 90 (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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22B GLN* 5.0 6.8 + - - -
23B PRO* 5.1 2.1 - - - +
60B VAL* 3.7 33.0 - - + -
89B TYR* 1.3 72.6 - - - +
91B LYS* 1.3 73.4 + - - +
92B ASN 5.5 0.4 - - - -
93B THR* 3.9 28.0 - - - -
94B ASP 3.4 7.6 - - - -
95B LEU* 4.4 9.6 - - + -
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Residues in contact with LYS 91 (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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22B GLN* 3.0 35.8 + - - +
23B PRO* 3.9 24.7 - - + -
24B GLU* 3.5 24.1 + - - +
89B TYR 4.0 0.2 + - - -
90B PHE* 1.3 79.4 - - - +
92B ASN* 1.3 103.9 + - + +
93B THR 3.4 1.6 - - - -
94B ASP* 3.0 27.4 + - - +
96B TRP* 4.1 19.9 + - + +
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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