Contacts of the strand formed by residues 103 - 108 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A GLY 3.0 7.6 + - - +
73A MET* 3.2 28.1 - - + +
74A VAL 2.8 26.7 + - - +
102A ALA* 1.3 73.8 - - - +
104A CYS* 1.3 61.1 + - - +
105A PHE* 4.2 8.9 - - + -
124A TYR* 3.5 34.9 - - + +
128A ARG* 5.3 4.4 - - - +
112B TYR* 3.1 20.8 + - - +
116B PRO* 4.2 13.7 - - - +
119B GLN* 3.4 31.2 + - - +
120B LEU* 4.2 8.1 - - - +
123B ASP* 4.8 1.4 + - - -
175B ALA* 3.7 13.7 - - - +
177B ALA* 3.7 11.8 - - + +
179B THR* 4.6 0.2 - - - -
310B VAL* 4.6 1.1 - - - -
312B GLU* 2.8 35.6 + - - +
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Residues in contact with CYS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A VAL* 3.3 11.7 - - - -
87A ALA* 4.5 1.1 - - - +
89A ALA* 3.9 13.9 - - + -
90A VAL* 4.0 15.3 - - + -
93A HIS* 3.5 41.7 - - - -
102A ALA* 3.8 2.3 + - - -
103A ARG* 1.3 79.8 - - - +
105A PHE* 1.3 65.8 + - - +
109B GLU* 3.4 20.1 - - - +
112B TYR* 4.1 2.5 - - - -
179B THR* 3.5 24.7 + - - +
310B VAL* 3.6 7.1 - - + +
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Residues in contact with PHE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A MET* 4.2 7.2 - - - -
74A VAL 3.3 4.4 + - - -
75A ILE* 3.4 34.4 - - + -
76A VAL 3.1 21.8 + - - -
87A ALA* 3.7 9.9 - - - -
89A ALA* 3.5 5.3 - - - +
103A ARG* 4.2 15.3 - - + -
104A CYS* 1.3 83.6 - - - +
106A GLU* 1.3 70.8 + - - +
107A MET* 3.9 22.9 - - + -
107B MET* 3.9 17.0 - - + -
108B LYS 3.6 14.1 - - - +
109B GLU* 3.8 7.9 - - + -
112B TYR* 4.6 5.2 - + + -
113B ALA* 5.9 0.7 - - - -
116B PRO* 3.8 27.6 - - + -
120B LEU* 3.7 24.0 - - + -
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ILE* 5.0 0.2 - - - +
76A VAL* 3.1 24.9 - - + +
78A THR* 3.6 23.6 - - + +
81A ALA* 3.8 8.0 - - - +
82A VAL 5.6 0.3 + - - -
86A LYS 3.9 0.3 - - - +
87A ALA* 4.1 1.1 - - + -
88A ALA* 2.8 38.7 + - - +
105A PHE* 1.3 79.2 - - - +
107A MET* 1.3 66.3 + - - +
108A LYS* 5.9 4.1 - - + +
107B MET* 3.3 5.2 - - - -
108B LYS* 2.9 76.4 + - + +
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Residues in contact with MET 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ILE* 3.9 14.4 - - + -
76A VAL 2.9 7.8 + - - +
77A ALA* 3.5 1.6 - - - -
78A THR 3.4 17.8 + - - +
105A PHE* 3.9 16.6 - - + -
106A GLU* 1.3 79.9 - - - +
108A LYS* 1.3 60.5 + - - +
113A ALA* 3.4 27.2 - - + +
116A PRO* 4.0 3.6 - - - -
117A ALA* 3.6 38.1 - - - -
120A LEU* 3.9 22.0 - - + -
105B PHE* 4.0 15.7 - - + -
106B GLU 3.2 9.0 - - - +
107B MET* 3.7 26.9 - - + -
120B LEU* 4.6 1.8 - - + -
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Residues in contact with LYS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A THR 3.9 16.4 - - - +
79A GLU* 4.9 0.7 - - - +
81A ALA* 6.3 3.4 - - - -
106A GLU* 5.9 4.0 - - + +
107A MET* 1.3 74.8 - - - +
109A GLU* 1.3 67.1 + - - +
110A ALA 4.6 1.3 - - - +
113A ALA* 4.0 2.9 - - - -
81B ALA* 3.3 14.8 - - - +
83B ASP 2.9 26.1 + - - +
84B ALA* 3.9 17.7 - - - +
85B ALA* 3.7 18.6 - - - +
86B LYS 4.7 2.7 - - - +
87B ALA* 3.4 5.0 - - - +
105B PHE* 4.4 1.5 - - - +
106B GLU* 2.8 72.5 + - + +
108B LYS* 6.1 11.2 - - + +
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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