Contacts of the strand formed by residues 103 - 109 (chain B) in PDB entry 2P7I
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 TYR 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B ASN* 3.3 31.9 - - - +
45B LEU 4.1 6.1 - - - -
46B LEU* 3.6 27.1 - - + +
67B THR* 3.5 35.8 + - + +
99B LEU* 3.7 20.7 - - + +
100B PRO* 3.4 30.8 - - - +
101B ARG* 3.1 29.9 - - + +
102B ARG* 1.3 76.2 - - - +
104B ASP* 1.3 62.2 + - - +
105B ASN 3.3 15.7 - - - +
106B ILE* 4.0 5.8 - - + -
129B TRP* 2.9 16.6 + - + +
130B LEU* 3.7 8.3 - - - +
131B ALA* 2.8 26.7 + - - +
134B GLY* 4.0 2.6 - - - -
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Residues in contact with ASP 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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41B ARG* 3.5 18.1 + - + +
42B PRO 3.5 22.7 - - - +
43B GLY* 3.3 5.9 - - - -
44B ASN* 2.9 41.9 + - - +
102B ARG 5.3 0.4 - - - +
103B TYR* 1.3 74.0 - - - +
105B ASN* 1.3 62.5 + - - +
131B ALA* 3.8 14.4 - - - +
132B GLU 4.7 4.7 - - - +
133B GLY 5.8 0.3 - - - -
134B GLY* 3.1 10.8 + - - -
135B ARG 2.9 22.1 + - - -
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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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40B PHE* 3.5 9.3 - - + -
41B ARG* 2.8 48.4 + - - +
42B PRO 4.6 0.2 + - - -
44B ASN 3.1 21.5 + - - +
45B LEU* 3.2 19.7 - - + -
46B LEU 2.8 25.6 + - - -
63B PHE* 3.3 16.3 - - - -
103B TYR* 3.9 1.6 - - - +
104B ASP* 1.3 82.4 - - - +
106B ILE* 1.3 64.9 + - - +
135B ARG 3.3 5.4 - - - -
137B PHE* 3.6 16.4 - - + -
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Residues in contact with ILE 106 (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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46B LEU* 3.3 15.9 - - + +
48B LEU* 3.6 30.1 - - + -
103B TYR* 4.0 10.5 - - + -
105B ASN* 1.3 79.3 - - - +
107B VAL* 1.3 61.3 + - - +
125B ILE* 3.8 9.6 - - + -
129B TRP* 3.7 39.0 - - + +
130B LEU* 3.7 24.9 - - + +
135B ARG 2.8 12.7 + - - +
136B LEU* 3.4 19.8 - - + +
137B PHE* 2.7 35.0 + - - -
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Residues in contact with VAL 107 (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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36B PHE* 4.2 15.3 - - + -
40B PHE* 5.0 1.1 - - + -
45B LEU* 3.7 28.0 - - + -
46B LEU 2.8 12.7 + - - +
47B GLU* 4.4 12.3 - - + -
48B LEU* 3.0 30.7 + - - +
55B PHE* 3.9 16.8 - - + -
59B LEU* 4.2 10.8 - - + -
106B ILE* 1.3 75.9 - - - +
108B LEU* 1.3 63.8 + - - +
109B THR* 3.8 31.4 - - + +
137B PHE* 3.8 10.3 - - + -
251B TRS 4.8 0.2 - - - +
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Residues in contact with LEU 108 (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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48B LEU* 3.5 30.5 - - + +
94B PHE* 4.7 0.2 - - + -
106B ILE 4.0 0.4 + - - -
107B VAL* 1.3 71.9 - - - +
109B THR* 1.3 60.1 + - - +
110B HIS 4.0 0.2 + - - -
111B VAL* 3.5 33.8 + - + -
112B LEU* 4.2 11.6 + - + +
121B LEU* 4.1 21.1 - - + -
122B LEU* 4.0 9.4 - - + -
125B ILE* 4.0 19.3 - - + -
136B LEU* 4.1 13.9 - - + -
137B PHE 2.9 11.4 + - - +
138B LEU* 3.6 25.1 - - + +
139B VAL 3.0 24.8 + - - +
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Residues in contact with THR 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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32B MSE 4.4 17.0 - - - -
36B PHE* 3.3 35.2 - - + -
48B LEU 4.9 0.2 + - - -
55B PHE* 4.1 6.1 - - + -
107B VAL* 3.8 14.9 - - + +
108B LEU* 1.3 73.8 - - - +
110B HIS* 1.3 70.4 + - - +
111B VAL* 3.2 5.2 + - - +
137B PHE 4.3 0.9 - - - +
139B VAL* 3.5 20.2 - - + -
251B TRS 2.9 51.1 + - - -
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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