Contacts of the strand formed by residues 108 - 113 (chain B) in PDB entry 2PDA
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 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B THR 3.6 7.2 + - - +
82B THR* 3.0 25.1 - - - +
106B PRO 3.9 8.3 - - - +
107B GLY* 1.3 80.0 - - - +
109B PHE* 1.3 74.4 + - - +
110B HIS* 3.2 32.3 - - + +
156B ALA* 3.9 17.9 - - + +
157B HIS* 3.7 32.1 - - + +
160B ALA* 3.9 16.4 - - + -
167B PHE* 3.1 10.8 - - + +
169B HIS* 5.2 0.9 - - + -
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Residues in contact with PHE 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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68B ALA* 5.2 2.9 - - + -
71B VAL* 3.8 24.9 - - + -
83B THR* 3.4 26.9 - - + -
85B THR* 5.1 1.3 - - + -
90B LEU* 4.6 7.9 - - + -
93B MET* 3.7 25.8 - - + -
97B MET* 3.7 30.5 - - + -
100B ILE* 4.2 14.4 - - + -
107B GLY* 5.2 1.3 - - - -
108B VAL* 1.3 88.3 - - - +
110B HIS* 1.3 57.1 + - - +
111B VAL* 3.9 7.9 + - + -
138B PHE* 3.7 27.1 - + + -
167B PHE 2.8 9.6 + - - +
168B MET* 3.1 10.6 - - + +
169B HIS* 2.7 32.9 + - - +
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Residues in contact with HIS 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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14B THR* 3.4 15.7 - - - -
18B ALA* 4.1 9.2 - - + +
36B MET* 3.8 13.4 - - + +
82B THR* 3.5 17.5 - - + +
83B THR 3.1 6.5 + - - +
84B PHE* 3.3 23.4 - + + -
85B THR* 3.1 21.7 + - - +
108B VAL* 3.2 19.0 - - + +
109B PHE* 1.3 70.1 - - - +
111B VAL* 1.3 60.3 + - - +
153B ALA* 3.6 16.1 - - + +
157B HIS* 3.2 30.3 + - - -
169B HIS* 2.9 41.6 - + + +
171B PHE* 4.8 1.6 - - + -
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Residues in contact with VAL 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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85B THR* 3.1 31.0 - - + +
86B ALA* 4.7 0.7 - - - -
90B LEU* 4.0 6.7 - - + -
109B PHE* 4.3 6.5 - - + +
110B HIS* 1.3 79.2 - - - +
112B THR* 1.3 60.7 + - - +
113B ALA* 3.1 15.9 + - - +
129B ASP* 4.5 4.7 - - - +
130B ILE* 3.9 15.0 - - + -
168B MET* 3.8 31.9 - - + -
169B HIS 2.8 6.7 + - - +
170B PHE* 3.0 34.3 - - + -
171B PHE* 3.2 5.5 + - - -
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Residues in contact with THR 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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11B ASN* 3.2 30.5 - - - +
32B PRO* 3.2 15.2 - - - +
33B SER* 3.2 21.4 + - - -
36B MET* 3.7 10.5 - - + -
85B THR 3.3 3.0 + - - -
86B ALA* 3.4 11.0 - - - +
111B VAL* 1.3 70.8 - - - +
113B ALA* 1.3 66.9 + - - +
114B ARG* 3.1 5.4 + - - +
171B PHE* 3.4 27.4 - - + -
173B GLY* 4.0 5.6 - - - -
177B SER* 3.7 15.3 - - - -
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Residues in contact with ALA 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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111B VAL* 3.1 9.0 + - - -
112B THR* 1.3 69.4 - - - +
114B ARG* 1.3 58.4 + - - +
126B ASP 3.1 23.4 + - - +
127B HIS* 3.9 20.0 - - + -
129B ASP* 3.5 14.4 - - - +
130B ILE* 4.1 10.1 - - + -
170B PHE* 4.2 5.4 - - + -
171B PHE 2.9 16.2 + - - +
172B ASP* 4.3 1.3 - - - -
173B GLY* 2.8 27.0 + - - -
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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