Contacts of the strand formed by residues 61 - 66 (chain B) in PDB entry 1P1C
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 GLY 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLY* 1.3 75.0 - - - -
62B ARG* 1.3 60.0 + - - -
63B VAL* 3.5 4.3 + - - +
81B PRO 4.7 1.4 + - - -
82B ILE* 3.9 0.6 - - - +
83B LYS* 3.2 50.0 + - - +
84B GLU 3.3 9.2 + - - +
129B ASP* 3.2 10.1 - - - -
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Residues in contact with ARG 62 (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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61B GLY* 1.3 70.3 - - - -
63B VAL* 1.3 59.5 + - - +
83B LYS* 3.6 24.8 - - - +
84B GLU* 2.6 39.2 + - + -
86B TRP* 3.0 51.0 - - + +
127B HIS* 3.1 55.2 + - - +
128B PHE* 3.4 15.1 - - + +
129B ASP* 2.8 38.1 + - - +
130B GLY 3.7 0.5 + - - -
160B LYS* 4.4 4.9 - - - +
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ALA* 4.0 29.8 - - + +
57B ALA* 4.5 0.4 - - - -
60B GLY 4.3 5.4 - - - +
61B GLY 3.8 2.5 - - - +
62B ARG* 1.3 76.9 - - - +
64B LEU* 1.3 70.4 + - - +
65B GLU* 4.0 2.2 - - + +
77B VAL* 4.5 14.4 - - + -
82B ILE* 3.2 39.5 - - + -
84B GLU 3.2 9.2 + - - +
85B HIS* 3.7 10.5 - - + +
86B TRP* 2.8 31.4 + - - +
128B PHE* 4.1 2.5 - - - -
130B GLY 3.3 13.0 - - - +
132B LEU* 5.3 0.4 - - + -
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Residues in contact with LEU 64 (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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63B VAL* 1.3 74.7 - - - +
65B GLU* 1.3 54.5 + - - +
66B VAL* 4.4 7.6 - - + -
86B TRP* 3.2 18.8 - - + +
88B ILE* 4.5 17.3 - - + -
112B LEU* 5.5 0.7 - - + -
120B ALA* 6.3 0.4 - - + -
123B LEU* 4.0 14.6 - - + -
128B PHE* 3.7 46.4 - - + -
130B GLY 2.8 8.9 + - - -
131B ILE* 3.1 19.4 - - + -
132B LEU* 2.6 35.0 + - - +
150B PHE* 4.2 17.0 - - + -
158B LEU* 4.0 17.0 - - + -
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Residues in contact with GLU 65 (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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63B VAL* 4.0 2.0 + - + -
64B LEU* 1.3 74.3 - - - +
66B VAL* 1.3 63.0 + - - +
67B GLY 3.8 19.2 - - - +
68B PHE* 4.7 5.4 - - - +
73B ALA* 4.1 6.2 - - - +
74B ALA* 3.3 33.0 + - - +
77B VAL* 4.2 4.7 - - - +
85B HIS* 2.7 37.6 + - + +
86B TRP 2.7 11.3 + - - +
87B ILE* 3.0 36.3 - - + +
88B ILE 3.0 3.4 + - - -
132B LEU* 3.3 26.2 - - + +
134B ASP* 6.4 0.2 - - + -
2002B SAH 4.8 1.9 + - - -
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Residues in contact with VAL 66 (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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64B LEU* 4.4 11.7 - - + -
65B GLU* 1.3 74.5 - - - +
67B GLY* 1.3 66.9 + - - +
88B ILE* 3.9 19.3 - - + +
116B TRP* 4.0 25.4 - - + -
131B ILE* 5.3 0.2 - - + -
132B LEU 2.7 16.5 + - - +
133B TYR* 3.9 11.7 - - + -
134B ASP* 3.0 27.4 + - - +
135B THR* 3.5 17.7 - - - +
150B PHE* 3.8 32.1 - - + -
2002B SAH 4.2 7.4 - - + -
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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