Contacts of the strand formed by residues 103 - 108 (chain B) in PDB entry 1XPM
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 ARG 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A TYR* 3.1 20.6 + - - +
116A PRO* 4.3 13.4 - - - +
119A GLN* 3.3 30.7 + - - +
120A LEU* 4.2 8.5 - - - +
123A ASP* 4.8 1.4 + - - -
175A ALA* 3.8 13.1 - - - +
177A ALA* 3.6 11.2 - - + +
179A THR* 4.6 0.2 - - - -
310A VAL* 4.6 1.1 - - - -
312A GLU* 2.8 36.8 + - - +
72B GLY 3.0 8.1 + - - +
73B MET* 3.2 27.0 - - + +
74B VAL 2.8 26.4 + - - +
102B ALA* 1.3 73.4 - - - +
104B CYS* 1.3 61.5 + - - +
105B PHE* 4.2 9.6 - - + -
124B TYR* 3.5 34.5 - - + +
128B ARG* 5.5 3.2 - - - +
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Residues in contact with CYS 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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109A GLU* 3.3 20.1 - - - +
112A TYR* 4.2 2.6 - - - -
179A THR* 3.5 23.8 + - - +
310A VAL* 3.7 7.0 - - + +
74B VAL* 3.3 11.7 - - - -
87B ALA* 4.5 1.3 - - - +
89B ALA* 3.9 13.9 - - + -
90B VAL* 4.1 15.5 - - + -
93B HIS* 3.5 41.7 - - - -
102B ALA 3.9 2.5 + - - -
103B ARG* 1.3 80.0 - - - +
105B PHE* 1.3 65.8 + - - +
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Residues in contact with PHE 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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107A MET* 4.0 15.9 - - + -
108A LYS 3.6 13.5 - - - +
109A GLU* 3.8 8.5 - - + -
112A TYR* 4.6 3.4 - + + -
113A ALA* 5.9 0.9 - - - -
116A PRO* 3.7 26.7 - - + -
120A LEU* 3.7 23.3 - - + -
73B MET* 4.2 14.6 - - - -
74B VAL 3.3 4.0 + - - -
75B ILE* 3.4 34.1 - - + -
76B VAL 3.0 21.5 + - - -
87B ALA* 3.7 10.8 - - - -
89B ALA* 3.5 5.0 - - - +
103B ARG* 4.2 7.9 - - + -
104B CYS* 1.3 84.8 - - - +
106B GLU* 1.3 72.2 + - - +
107B MET* 3.9 23.3 - - + -
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Residues in contact with GLU 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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107A MET* 3.2 5.2 - - - -
108A LYS* 2.8 71.1 + - + +
51B ILE* 5.1 0.2 - - - +
76B VAL* 3.1 22.4 - - + +
78B THR* 3.6 23.1 - - + +
81B ALA* 3.9 5.9 - - - +
82B VAL 5.5 0.5 + - - -
83B ASP 4.9 0.7 + - - +
86B LYS 3.9 3.8 - - - +
87B ALA* 3.5 8.1 - - + -
88B ALA* 2.7 39.5 + - - +
105B PHE* 1.3 78.9 - - - +
107B MET* 1.3 66.5 + - - +
108B LYS* 5.9 2.6 - - + +
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Residues in contact with MET 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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105A PHE* 3.9 15.3 - - + -
106A GLU 3.3 9.4 - - - +
107A MET* 3.7 28.0 - - + -
120A LEU* 4.7 0.7 - - + -
75B ILE* 3.9 13.0 - - + -
76B VAL 2.9 8.4 + - - +
77B ALA* 3.5 2.0 - - + -
78B THR 3.5 17.5 + - - +
105B PHE* 3.9 15.9 - - + -
106B GLU* 1.3 81.0 - - - +
108B LYS* 1.3 61.1 + - - +
113B ALA* 3.4 25.5 - - + +
116B PRO* 4.0 4.3 - - + -
117B ALA* 3.5 40.4 - - - -
120B LEU* 3.9 22.4 - - + -
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Residues in contact with LYS 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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81A ALA* 3.8 7.4 - - + +
83A ASP 2.6 26.4 + - - +
84A ALA* 3.6 21.3 - - - +
85A ALA* 3.8 12.3 - - - +
86A LYS 3.4 15.7 + - - -
87A ALA* 3.4 10.5 - - - +
105A PHE* 3.6 1.7 - - - +
106A GLU* 2.9 87.6 + - + +
108A LYS* 6.1 10.8 - - + +
78B THR 3.8 16.6 - - - +
79B GLU* 4.8 0.2 - - - -
106B GLU* 5.8 3.1 - - + +
107B MET* 1.3 73.9 - - - +
109B GLU* 1.3 64.8 + - - +
110B ALA 4.7 0.9 - - - +
113B ALA* 4.1 4.2 - - - +
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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