Contacts of the strand formed by residues 85 - 93 (chain B) in PDB entry 3LQM
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 HIS 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56B TYR* 5.6 2.2 - + + -
57B LEU 4.8 12.6 - - - -
79B LEU* 3.6 38.7 - - + +
80B SER* 2.8 55.5 + - - -
83B GLY* 3.5 15.9 + - - -
84B ASP* 1.3 77.8 - - - +
86B THR* 1.3 63.6 + - - +
87B LEU* 4.3 8.3 - - + -
104B THR* 3.1 9.0 - - - +
105B PHE* 2.8 46.2 + - + +
107B PRO* 3.8 6.3 - - - +
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Residues in contact with THR 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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56B TYR* 3.4 2.9 - - - +
57B LEU* 2.8 57.5 + - + +
62B PHE* 3.9 10.1 - - + -
84B ASP 4.9 1.9 + - - -
85B HIS* 1.3 77.5 + - - +
87B LEU* 1.3 64.5 + - - +
102B GLN* 3.5 39.5 - - + +
103B ILE 3.5 6.1 - - - +
104B THR* 4.2 11.9 - - + +
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Residues in contact with LEU 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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29B MET* 3.3 34.1 - - + -
38B LEU* 4.4 17.5 - - + -
55B GLN 3.3 6.3 - - - +
56B TYR* 3.5 23.6 - - + -
62B PHE* 4.7 0.4 - - - -
76B PHE* 4.1 17.0 - - + -
79B LEU* 3.9 20.0 - - + -
85B HIS* 4.4 7.0 - - + -
86B THR* 1.3 84.2 - - - +
88B ARG* 1.3 62.7 + - - +
101B VAL 4.0 0.2 - - - +
102B GLN* 3.2 6.7 - - - +
103B ILE* 2.9 46.9 + - + +
105B PHE* 4.7 7.9 - - + -
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Residues in contact with ARG 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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38B LEU* 4.9 2.4 - - - +
53B THR 4.0 0.3 - - - +
54B ALA* 3.3 3.7 - - - +
55B GLN* 2.7 62.4 + - + +
62B PHE* 3.4 47.3 - - + +
87B LEU* 1.3 78.5 - - - +
89B VAL* 1.3 61.9 + - - +
100B TRP* 3.4 50.9 - - + +
101B VAL 3.2 13.0 - - - +
102B GLN* 4.1 15.0 - - + +
611B SO4 3.1 44.3 + - - -
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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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24B PRO* 4.0 17.1 - - + +
27B VAL* 3.8 35.0 - - + -
38B LEU* 4.3 7.9 - - + -
40B TRP* 4.2 30.7 - - + -
52B PHE* 4.3 1.3 - - + -
53B THR 3.2 17.7 - - - +
54B ALA* 4.3 6.3 - - + -
88B ARG* 1.3 77.1 - - - +
90B ARG* 1.3 69.5 + - - +
100B TRP* 3.5 3.3 - - - -
101B VAL* 2.9 37.7 + - + +
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Residues in contact with ARG 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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24B PRO* 3.7 9.9 - - - -
52B PHE* 3.3 7.6 - - - +
53B THR* 3.1 31.7 + - - +
89B VAL* 1.3 78.5 - - - +
91B ALA* 1.3 64.2 + - - +
92B GLU* 3.2 25.2 + - - +
97B HIS* 3.4 40.4 + - - +
98B SER* 3.5 12.4 + - - +
99B ASP 3.5 15.9 - - - +
100B TRP* 3.5 48.8 - - + +
609B SO4 2.9 41.2 + - - -
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Residues in contact with ALA 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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21B VAL* 3.8 9.6 - - + -
22B PRO 3.3 26.2 - - - +
24B PRO* 3.7 4.1 - - + +
43B PRO* 5.2 0.2 - - + -
50B LEU* 4.5 8.5 - - + -
51B THR 3.4 5.4 - - - +
52B PHE* 3.8 22.0 - - + -
90B ARG* 1.3 73.4 - - - +
92B GLU* 1.3 68.7 + - - +
97B HIS* 3.3 1.2 - - - +
98B SER* 2.8 30.9 + - - +
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Residues in contact with GLU 92 (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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21B VAL* 4.4 1.3 - - - -
49B GLN 4.6 0.3 - - - +
50B LEU* 3.5 7.4 - - - -
51B THR* 2.8 50.2 + - - +
52B PHE 3.9 4.3 - - - -
53B THR* 2.8 34.4 + - - +
68B GLN* 3.5 20.4 - - + +
90B ARG* 3.2 26.5 + - - +
91B ALA* 1.3 80.5 - - - +
93B PHE* 1.3 62.3 + - - +
94B ALA 5.4 2.7 - - - +
96B GLU 3.4 4.5 - - - -
97B HIS* 3.0 30.7 + - + +
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Residues in contact with PHE 93 (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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21B VAL* 4.2 7.8 - - + +
45B PHE* 3.5 23.6 - + + -
47B LYS* 3.8 26.5 - - + -
48B GLY* 3.8 26.9 - - - -
49B GLN 3.5 27.4 - - - -
50B LEU* 3.9 11.2 - - + -
92B GLU* 1.3 74.8 - - - +
94B ALA* 1.3 84.7 + - + +
96B GLU* 2.9 31.8 + - - +
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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