Contacts of the strand formed by residues 101 - 105 (chain B) in PDB entry 2ADM
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 LEU 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B ALA* 4.0 11.7 - - + -
36B GLU 3.4 28.7 - - - +
37B ALA* 4.1 6.7 - - + -
42B ARG 3.3 6.5 + - - +
43B VAL* 3.5 17.4 - - + -
44B LEU* 2.9 24.8 + - - +
57B PHE* 3.3 43.3 - - + -
99B PHE* 3.6 0.9 - - - +
100B ASP* 1.3 81.8 - - - +
102B ILE* 1.3 71.2 + - - +
103B LEU* 4.0 14.1 - - + -
159B VAL* 3.2 29.4 - - + +
161B VAL* 4.8 1.3 - - + -
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Residues in contact with ILE 102 (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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44B LEU* 3.3 28.3 - - + +
46B PRO* 3.8 24.0 - - + -
90B PHE* 5.2 0.7 - - + -
99B PHE* 4.2 7.9 - - + -
101B LEU* 1.3 79.8 - - - +
103B LEU* 1.3 63.5 + - - +
150B ALA* 3.5 35.4 - - + +
153B LEU* 4.2 12.6 - - + -
154B LEU* 3.6 15.0 - - + -
159B VAL 3.0 6.1 + - - -
160B LEU* 3.2 11.5 - - + +
161B VAL 2.9 26.7 + - - +
162B PHE* 3.9 17.9 - - + -
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Residues in contact with LEU 103 (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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31B MET* 4.6 8.7 - - + +
32B VAL* 4.8 5.2 - - + -
35B ALA* 3.8 23.8 - - + -
43B VAL* 4.3 8.3 - - + -
44B LEU 3.0 7.4 + - - +
45B GLU* 3.3 11.8 - - + +
46B PRO* 3.2 20.6 - - - +
53B PHE* 3.8 44.2 - - + +
54B LEU* 5.0 0.4 - - + +
57B PHE* 3.9 24.7 - - + -
101B LEU* 4.0 12.6 - - + -
102B ILE* 1.3 76.6 - - - +
104B GLY* 1.3 59.4 + - - +
161B VAL* 3.5 23.1 - - + +
162B PHE* 3.9 3.6 - - - -
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Residues in contact with GLY 104 (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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31B MET* 3.6 5.0 - - - +
45B GLU* 4.4 4.5 - - - -
46B PRO* 4.7 6.1 - - - -
53B PHE* 3.8 21.7 - - - -
103B LEU* 1.3 78.7 - - - +
105B ASN* 1.3 61.0 + - - -
106B PRO* 3.8 4.0 - - - -
161B VAL 3.3 6.9 + - - -
162B PHE* 3.3 30.5 - - - -
163B VAL 3.4 4.2 + - - -
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Residues in contact with ASN 105 (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* 4.3 10.2 - - - -
23B THR* 3.1 26.9 + - - +
46B PRO 5.0 3.7 + - - +
47B ALA* 4.8 3.1 - - - +
53B PHE* 3.8 8.9 - - + -
104B GLY* 1.3 75.1 - - - +
106B PRO* 1.3 61.5 + - - +
107B PRO* 4.2 1.0 - - - +
108B TYR* 2.8 35.9 + - - -
163B VAL* 3.4 14.9 + - + -
196B PHE* 4.0 13.9 - - - -
500B SAM 3.0 44.7 + - + +
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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