Contacts of the strand formed by residues 103 - 108 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72C GLY 3.0 8.3 + - - +
73C MET* 3.2 22.6 - - + +
74C VAL 2.9 26.4 + - - +
102C ALA* 1.3 73.0 - - - +
104C CYS* 1.3 61.2 + - - +
105C PHE* 4.2 9.8 - - + -
124C TYR* 3.6 32.9 - - + +
128C ARG* 5.5 3.2 - - - +
112D TYR* 3.1 20.8 + - - +
116D PRO* 4.3 12.8 - - - +
119D GLN* 3.3 29.1 + - - +
120D LEU* 4.0 15.6 - - - +
123D ASP* 4.8 1.2 + - - -
175D ALA* 3.8 12.9 - - - +
177D ALA* 3.7 11.2 - - + +
179D THR* 4.5 0.2 - - - -
310D VAL* 4.6 1.1 - - - -
312D GLU* 2.8 36.0 + - - +
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Residues in contact with CYS 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C VAL* 3.3 11.9 - - - -
87C ALA* 4.5 1.5 - - - +
89C ALA* 3.9 13.7 - - + -
90C VAL* 4.1 15.7 - - + -
93C HIS* 3.5 42.6 - - - -
102C ALA 3.8 2.5 + - - -
103C ARG* 1.3 79.6 - - - +
105C PHE* 1.3 65.3 + - - +
109D GLU* 3.3 20.4 - - - +
112D TYR* 4.2 2.8 - - - -
179D THR* 3.5 23.1 + - - +
310D VAL* 3.7 6.6 - - + +
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Residues in contact with PHE 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C MET* 4.2 14.6 - - - -
74C VAL 3.2 3.2 + - - -
75C ILE* 3.4 33.2 - - + -
76C VAL 3.0 21.5 + - - -
87C ALA* 3.7 10.5 - - - -
89C ALA* 3.5 5.5 - - - +
103C ARG* 4.2 8.1 - - + -
104C CYS* 1.3 84.2 - - - +
106C GLU* 1.3 72.7 + - - +
107C MET* 3.8 26.0 - - + -
107D MET* 4.1 17.7 - - + -
108D LYS 3.6 13.9 - - - +
109D GLU* 3.8 7.9 - - + -
112D TYR* 4.6 3.8 - + + -
113D ALA* 5.9 0.9 - - - -
116D PRO* 3.8 25.6 - - + -
120D LEU* 3.7 23.3 - - + -
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Residues in contact with GLU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ILE* 5.1 0.2 - - - +
76C VAL* 3.1 22.9 - - + +
78C THR* 3.6 23.8 - - + +
81C ALA* 3.9 8.4 - - - +
82C VAL 5.5 0.5 + - - -
83C ASP 5.8 0.2 + - - -
86C LYS 3.9 0.5 - - - +
87C ALA* 4.0 1.6 - - + -
88C ALA* 2.8 38.1 + - - +
105C PHE* 1.3 78.7 - - - +
107C MET* 1.3 66.4 + - - +
108C LYS* 5.9 2.7 - - + +
107D MET* 3.3 5.0 - - - -
108D LYS* 2.8 74.7 + - + +
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Residues in contact with MET 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ILE* 3.9 13.9 - - + -
76C VAL 2.9 8.4 + - - +
77C ALA* 3.5 2.2 - - + -
78C THR 3.5 17.2 + - - +
105C PHE* 3.8 26.5 - - + -
106C GLU* 1.3 79.4 - - - +
108C LYS* 1.3 61.8 + - - +
113C ALA* 3.4 25.9 - - + +
116C PRO* 4.0 4.5 - - + -
117C ALA* 3.6 41.3 - - - -
120C LEU* 4.0 16.2 - - + -
105D PHE* 4.0 23.3 - - + -
106D GLU 3.3 5.6 - - - +
107D MET* 3.8 18.6 - - + -
120D LEU* 4.8 0.7 - - + -
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Residues in contact with LYS 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C THR 3.7 18.4 - - - +
79C GLU* 4.7 0.2 - - - -
106C GLU* 5.7 3.4 - - + +
107C MET* 1.3 75.6 - - - +
109C GLU* 1.3 64.0 + - - +
110C ALA 4.6 1.1 - - - +
113C ALA* 4.0 3.1 - - - -
81D ALA* 3.7 7.9 - - - +
83D ASP 2.7 27.8 + - - +
84D ALA* 3.9 12.6 - - - +
85D ALA* 3.3 26.7 - - - +
86D LYS 3.7 5.9 + - - -
87D ALA* 3.4 8.2 - - - +
105D PHE* 3.6 1.7 - - - +
106D GLU* 2.8 83.5 + - + +
108D LYS* 6.3 3.1 - - + -
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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