Contacts of the strand formed by residues 80 - 90 (chain B) in PDB entry 3LZP
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 ILE 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B GLU* 3.8 33.9 - - + +
72B LEU 3.3 5.8 - - - +
73B LYS* 3.7 37.2 - - + +
78B GLY 3.5 10.7 + - - +
79B ALA* 1.3 80.3 - - - +
81B LYS* 1.3 65.6 + - - +
82B ARG* 4.9 7.0 - - + +
107B LYS* 5.3 4.0 - - - -
110B PHE* 3.5 7.5 - - - -
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Residues in contact with LYS 81 (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 TYR* 4.3 12.7 - - + +
71B GLU* 3.4 3.6 - - - +
72B LEU* 2.8 47.6 + - + +
80B ILE* 1.3 74.6 - - - +
82B ARG* 1.3 66.3 + - - +
100B ILE* 3.7 21.0 - - + +
101B ALA* 2.6 31.7 + - - +
102B MET* 5.4 0.2 - - - -
105B ASP* 2.6 26.6 + - - -
107B LYS* 4.8 9.2 - - - +
110B PHE* 3.7 31.0 - - + -
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Residues in contact with ARG 82 (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 TYR* 3.2 19.3 + - - +
71B GLU* 2.8 43.0 + - + +
80B ILE* 4.9 6.0 - - + +
81B LYS* 1.3 82.0 - - - +
83B GLY* 1.3 59.0 + - - +
120B TYR* 3.7 20.0 + - - -
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Residues in contact with GLY 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ALA* 3.2 9.9 - - - +
70B TYR* 2.9 46.6 + - - -
82B ARG* 1.3 76.8 - - - +
84B THR* 1.3 64.4 + - - -
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Residues in contact with THR 84 (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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67B THR* 6.3 2.5 - - + -
68B ILE 3.5 10.5 - - - +
69B ALA* 4.8 6.7 - - + -
70B TYR* 3.7 2.0 - - - -
83B GLY* 1.3 79.2 - - - +
85B LEU* 1.3 67.5 - - - +
86B MET* 4.1 18.0 + - - +
98B ALA* 3.7 16.1 - - - +
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Residues in contact with LEU 85 (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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43B LEU* 4.1 15.3 - - + +
44B GLU 4.9 0.7 - - - -
45B ALA* 3.7 32.5 - - + +
68B ILE* 3.0 35.3 + - + +
70B TYR* 3.7 21.5 - - + -
84B THR* 1.3 76.5 - - - +
86B MET* 1.3 65.5 + - - +
87B PRO* 4.4 2.8 - - - +
96B TYR* 3.9 17.3 - - + +
97B GLY 3.6 15.9 - - - +
98B ALA* 3.5 25.8 - - + +
119B PHE* 3.7 20.0 - - + -
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Residues in contact with MET 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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128A GLY* 4.5 14.6 - - - +
27B MET* 5.2 5.8 - - + -
32B ILE* 4.2 29.8 - - + -
33B ASP* 6.2 2.7 - - + -
84B THR* 4.5 18.8 - - - +
85B LEU* 1.3 80.6 - - - +
87B PRO* 1.3 80.4 - - + +
88B MET* 3.4 14.6 + - + +
96B TYR* 3.3 3.7 - - - -
97B GLY 2.9 31.8 + - - +
98B ALA* 6.2 0.2 - - + -
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Residues in contact with PRO 87 (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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65A TYR* 3.6 34.1 - - + +
128A GLY 4.5 2.6 - - - +
129A PHE* 3.7 22.8 - - + -
130A GLY 3.1 17.2 + - - -
27B MET* 5.3 0.5 - - - +
62B TRP* 4.0 2.9 - - + -
66B LEU 5.8 2.2 - - - +
85B LEU 4.4 2.2 - - - +
86B MET* 1.3 102.7 - - + +
88B MET* 1.3 59.3 - - - +
95B HIS 3.4 8.1 - - - +
96B TYR* 3.9 18.6 - - + -
127B GLN* 6.1 1.1 - - - +
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Residues in contact with MET 88 (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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129A PHE* 3.4 12.8 - - - -
130A GLY* 3.1 24.9 - - - +
131A ARG* 4.1 1.3 - - - +
132A HIS* 3.2 15.5 - - + +
25B ILE* 4.6 0.2 - - - -
27B MET* 3.3 28.9 - - - +
33B ASP* 5.0 4.3 - - - +
42B HIS* 3.7 8.1 - - + -
86B MET* 3.4 24.7 - - + +
87B PRO* 1.3 75.4 - - - +
89B VAL* 1.3 59.1 + - - +
93B GLY 4.2 0.2 - - - +
94B PRO* 3.2 3.6 - - - +
95B HIS* 2.9 41.6 + - + +
97B GLY 3.5 20.6 - - - +
200B CU 2.3 31.6 - - - -
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Residues in contact with VAL 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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55A ASN 3.1 28.7 - - - +
56A GLY 3.9 6.5 - - - -
57A PHE* 3.8 14.1 - - + -
129A PHE* 3.8 16.6 - - + -
130A GLY 2.9 17.4 + - - +
131A ARG* 3.3 12.8 - - + +
132A HIS* 2.9 27.9 + - - -
139A VAL* 4.2 4.2 - - + +
142A TRP* 4.0 11.7 - - + -
88B MET* 1.3 75.4 - - - +
90B ALA* 1.3 70.7 + - - +
93B GLY 3.6 16.8 - - - -
94B PRO* 3.8 2.7 - - + -
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Residues in contact with ALA 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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56A GLY* 3.6 2.3 - - - -
132A HIS* 3.4 34.1 - - + +
137A THR* 3.6 10.1 - - - +
139A VAL* 3.3 13.8 - - - +
44B GLU* 5.1 0.7 - - - +
89B VAL* 1.3 79.2 - - - +
91B ASP* 1.3 64.9 + - - +
92B ASP* 3.0 17.7 - - - +
93B GLY 2.9 21.7 + - - -
95B HIS* 3.9 7.4 - - + -
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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