Contacts of the strand formed by residues 2 - 10 (chain C) in PDB entry 1XHO
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 VAL 2 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A VAL* 4.0 25.1 - - + -
2B VAL* 4.1 19.2 - - + +
42B ILE* 3.6 21.7 - - + +
94B ASN* 3.1 28.7 + - - -
1C MSE 1.3 71.9 - - - +
3C TRP* 1.3 73.1 + - - +
42C ILE* 3.8 19.3 - - + -
92C HIS* 4.5 8.5 - - + -
93C VAL 3.4 9.4 - - - +
94C ASN* 3.1 21.5 - - - +
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Residues in contact with TRP 3 (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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39B ASP 3.2 24.7 - - - -
40B ASP 4.4 1.8 - - - -
41B ILE 3.6 24.0 - - - -
42B ILE* 3.8 17.5 - - - -
94B ASN* 3.1 27.1 - - + -
1C MSE 3.8 13.4 + - - +
2C VAL* 1.3 82.8 + - - +
4C ALA* 1.3 63.0 + - - +
92C HIS* 3.6 1.9 - - - -
93C VAL* 2.9 34.6 + - - +
95C THR* 3.9 12.1 - - + +
97C LYS 3.5 26.0 + - - -
98C ASP* 4.3 4.0 + - - +
99C LYS* 3.6 45.9 - - + +
102C ILE* 4.0 21.8 - - + -
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Residues in contact with ALA 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 3.1 31.7 + - + +
43B SER* 3.9 12.3 - - - -
70B ALA* 3.7 16.2 + - + +
3C TRP* 1.3 77.6 - - - +
5C ILE* 1.3 63.4 + - - +
90C MSE 4.7 2.2 - - + -
91C MSE 3.2 7.6 - - - +
92C HIS* 4.0 11.0 - - + +
102C ILE* 4.0 6.1 - - - +
104C HIS* 3.4 17.2 - - - -
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Residues in contact with ILE 5 (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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70B ALA* 4.6 1.3 - - - -
4C ALA* 1.3 75.5 - - - +
6C ARG* 1.3 64.6 + - - +
30C MSE 3.4 23.5 - - + +
34C ASN* 3.7 19.1 - - + +
36C LEU* 3.4 32.8 - - + -
90C MSE 3.4 2.3 - - - -
91C MSE 2.6 51.8 + - + +
93C VAL* 3.9 21.5 - - + -
102C ILE* 3.8 16.6 - - + -
103C LYS 3.3 26.2 - - - +
104C HIS* 3.7 3.8 - - - +
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Residues in contact with ARG 6 (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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70B ALA* 3.8 11.7 - - + -
71B LEU* 2.9 49.0 + - - +
72B MSE 3.6 14.2 - - - +
5C ILE* 1.3 73.7 - - - +
7C GLY* 1.3 71.4 + - - +
8C ALA* 3.6 27.7 - - - +
30C MSE 3.8 6.2 - - - +
88C ARG* 3.7 24.8 - - - +
89C VAL 3.2 12.8 - - - -
90C MSE 4.4 4.9 - - + +
104C HIS* 3.0 23.5 + - + +
105C VAL 3.0 23.1 + - - -
106C TYR* 3.7 30.9 + - - +
113C LEU* 4.8 1.8 - - - +
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Residues in contact with GLY 7 (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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6C ARG* 1.3 83.4 + - - +
8C ALA* 1.3 59.4 + - - -
26C LEU* 3.9 8.1 - - - -
30C MSE 3.7 20.3 - - - +
88C ARG* 3.3 3.8 - - - -
89C VAL 2.8 33.1 + - - -
105C VAL 3.1 11.0 - - - -
106C TYR* 5.3 0.2 - - - -
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Residues in contact with ALA 8 (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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6C ARG* 3.6 17.7 - - - +
7C GLY* 1.3 76.1 - - - +
9C THR* 1.3 63.5 + - - +
26C LEU* 3.7 7.4 - - - +
86C CYS* 4.4 0.7 - - - -
87C ILE 3.2 9.9 - - - +
88C ARG* 4.1 6.1 - - + -
105C VAL 2.9 7.0 + - - +
106C TYR* 3.5 10.8 - - + -
107C LEU 2.8 25.5 + - - -
110C ALA* 3.4 18.2 - - + -
113C LEU* 4.0 9.0 - - + -
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Residues in contact with THR 9 (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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8C ALA* 1.3 76.4 - - - +
10C THR* 1.3 70.8 + - - +
22C GLU* 3.7 31.1 + - + +
26C LEU* 3.7 22.0 - - + -
86C CYS* 3.3 6.4 - - - -
87C ILE* 2.8 48.6 + - + +
107C LEU* 3.4 19.6 - - - +
108C ASN* 3.0 23.6 + - - -
110C ALA* 3.4 1.5 - - - +
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Residues in contact with THR 10 (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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9C THR* 1.3 80.5 + - - +
11C VAL* 1.3 72.2 + - - +
22C GLU* 3.9 2.9 - - - +
83C LEU* 3.8 20.2 - - + -
84C GLU 4.0 9.6 - - - +
85C LYS* 3.1 12.1 - - - +
86C CYS* 4.3 1.1 - - - -
87C ILE 4.9 0.2 - - - +
107C LEU 3.9 2.4 + - - -
108C ASN* 2.8 28.5 + - - +
109C GLY* 2.7 31.6 + - - -
110C ALA 3.5 19.3 - - - +
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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