Contacts of the strand formed by residues 82 - 92 (chain B) in PDB entry 2ANL
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 VAL 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B TRP* 4.7 18.8 - - + +
74B GLU* 2.7 37.5 - - - +
75B ILE* 2.8 35.3 + - + +
77B TYR* 4.0 12.8 - - + -
81B THR* 1.3 77.7 - - - +
83B ARG* 1.3 58.8 + - - +
103B ILE* 6.2 2.7 - - + -
105B VAL* 4.3 19.5 - - + -
107B ASP 3.8 3.1 - - - -
108B THR* 4.7 12.8 - - - -
111B LEU* 4.3 25.1 - - + -
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Residues in contact with ARG 83 (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 VAL 3.9 5.8 - - - +
74B GLU* 3.2 31.7 + - + -
81B THR* 4.7 10.4 - - + +
82B VAL* 1.3 80.2 - - - +
84B GLY* 1.3 59.3 + - - +
103B ILE* 5.2 2.2 - - - -
105B VAL* 3.4 5.7 - - - +
106B THR* 2.8 22.4 + - - -
107B ASP* 3.1 44.9 + - + +
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Residues in contact with GLY 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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72B LYS* 3.4 7.6 - - - +
73B VAL 3.2 25.3 + - - -
83B ARG* 1.3 76.4 - - - +
85B PHE* 1.3 75.2 + - - +
103B ILE* 4.5 2.0 - - - +
104B GLU 3.2 13.7 - - - -
105B VAL* 4.3 0.2 - - - -
106B THR* 3.9 8.5 - - - -
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Residues in contact with PHE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B SER* 4.8 1.3 - - - -
46B LYS* 4.4 22.0 - - + -
66B TYR* 5.4 3.1 - - - -
70B GLY* 3.4 29.4 - - - +
71B THR 3.1 16.4 - - - +
72B LYS* 3.9 4.3 - - + +
73B VAL* 4.3 2.2 - - - +
84B GLY* 1.3 80.9 - - - +
86B PHE* 1.3 69.4 + - - +
87B SER* 3.3 1.9 + - - -
103B ILE* 3.9 7.8 - - - +
104B GLU* 2.9 72.0 + - + +
106B THR* 3.5 22.4 - - - -
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Residues in contact with PHE 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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39B ASN* 4.6 2.0 - - - -
69B ASP* 3.1 22.2 - - - +
70B GLY* 2.8 29.3 + - - -
71B THR* 2.9 28.8 + - + +
73B VAL* 3.7 31.2 - - + +
85B PHE* 1.3 74.3 - - - +
87B SER* 1.3 59.2 + - - +
101B LYS* 3.6 33.7 - - + -
102B PHE 3.3 15.9 - - - -
103B ILE* 3.7 17.5 - - + +
133B ILE 3.2 24.9 - - - -
134B GLY* 4.3 9.9 - - - -
136B ILE* 3.8 14.8 - - + -
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Residues in contact with SER 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B TYR* 5.4 0.2 - - - -
66B TYR* 4.3 14.8 + - - -
67B GLU 4.4 1.8 - - - -
69B ASP* 3.9 10.1 - - - +
70B GLY 5.1 0.5 + - - -
85B PHE* 3.3 8.7 + - - -
86B PHE* 1.3 77.0 + - - +
88B LYS* 1.3 61.3 + - - +
89B ASP 4.2 0.4 - - - -
101B LYS* 3.5 6.2 - - - +
102B PHE* 2.9 52.5 + - - -
104B GLU* 2.6 29.3 + - - +
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Residues in contact with LYS 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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65B SER 3.9 0.2 - - - +
66B TYR* 3.8 1.6 - - - -
67B GLU* 2.8 76.6 + - + +
69B ASP* 4.8 3.7 - - + +
87B SER* 1.3 76.8 - - - +
89B ASP* 1.4 57.3 + - - +
99B PRO* 4.2 30.4 - - + +
100B TYR* 3.1 24.2 - - - +
101B LYS* 4.3 11.9 - - + +
102B PHE* 4.3 0.4 - - - -
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Residues in contact with ASP 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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22B VAL* 5.2 0.4 - - + -
23B GLY* 3.3 16.2 - - - +
58B TYR* 3.0 29.6 + - + +
63B SER* 3.2 18.7 + - - -
65B SER* 3.3 13.9 - - - -
66B TYR* 3.1 23.2 + - + -
88B LYS* 1.4 73.9 - - - +
90B LEU* 1.3 82.0 + - - +
91B VAL* 3.7 0.6 + - - +
99B PRO* 3.1 6.4 - - - +
100B TYR* 2.6 38.7 + - - +
102B PHE* 3.6 18.1 - - + -
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Residues in contact with LEU 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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21B GLU 4.0 0.2 - - - +
22B VAL* 2.9 5.9 - - - +
23B GLY* 2.3 53.9 + - - +
24B ASP* 4.1 14.4 - - - +
26B HIS* 5.1 6.3 - - + -
65B SER* 4.4 9.6 - - - +
89B ASP* 1.3 93.8 + - - +
91B VAL* 1.3 60.0 + - - +
92B THR* 4.1 8.5 + - + -
97B SER* 4.0 15.9 - - - +
98B LEU* 2.9 46.9 - - - +
99B PRO* 3.8 5.8 - - + -
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Residues in contact with VAL 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 GLU 3.7 3.8 - - - +
22B VAL* 4.5 14.8 - - + -
40B LEU* 3.8 30.1 - - + -
89B ASP 3.7 1.5 + - - +
90B LEU* 1.3 70.7 - - - +
92B THR* 1.3 63.9 + - - +
93B LEU* 4.2 19.5 - - + +
97B SER 3.3 2.1 - - - -
98B LEU* 2.3 52.5 + - + +
100B TYR* 3.9 23.1 - - + -
102B PHE* 4.6 12.3 - - + -
124B LEU* 5.8 2.9 - - + -
139B ILE* 5.2 9.6 - - + -
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Residues in contact with THR 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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20B GLY* 4.4 0.7 - - - -
21B GLU* 2.8 56.0 + - + +
23B GLY 4.7 2.2 - - - +
26B HIS* 4.1 20.9 - - + +
90B LEU* 4.2 13.2 - - + +
91B VAL* 1.3 78.0 - - - +
93B LEU* 1.3 74.7 + - - +
94B GLY 3.7 10.0 + - - -
96B LEU 3.3 6.6 + - - -
97B SER* 3.2 26.5 + - - +
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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