Contacts of the helix formed by residues 93 - 99 (chain A) in PDB entry 1XDS
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 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A GLU* 4.9 0.6 + - - -
92A THR* 1.3 75.7 - - - +
94A LEU* 1.3 65.6 + - - +
96A MSE 3.2 9.4 + - - +
10B LEU* 3.7 22.9 - - + +
11B GLU 3.4 33.0 - - - +
12B PRO* 3.4 18.0 - - - +
13B THR* 4.1 13.6 + - - +
16B ASP* 2.7 35.6 + - - +
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Residues in contact with LEU 94 (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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33A LEU* 5.8 0.2 - - + -
77A GLY 3.9 10.1 - - - +
78A VAL* 4.0 25.4 - - + -
92A THR* 3.2 6.6 + - - +
93A ARG* 1.3 82.7 - - - +
95A GLY* 1.3 58.4 - - - +
97A LEU* 3.0 34.1 + - + +
98A LEU* 6.4 1.3 - - + -
16B ASP* 3.3 56.0 + - + +
19B VAL* 4.2 19.5 - - + -
20B LEU* 4.5 10.8 - - + +
24B LEU* 4.2 12.1 - - + -
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Residues in contact with GLY 95 (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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42A VAL* 3.5 19.1 - - - +
78A VAL* 3.4 31.4 - - - -
91A PRO* 3.9 6.1 - - - -
92A THR* 2.9 14.5 + - - -
94A LEU* 1.3 83.3 - - - +
96A MSE 1.3 55.5 + - - +
97A LEU 3.1 1.3 - - - -
98A LEU* 3.1 18.9 + - - +
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Residues in contact with MSE 96 (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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42A VAL* 4.7 1.1 - - - -
46A LEU* 3.9 32.1 - - + -
91A PRO* 3.8 25.8 - - + -
92A THR 3.1 17.3 + - - +
93A ARG 3.5 9.2 - - - +
94A LEU 3.1 1.4 + - - -
95A GLY* 1.3 72.4 - - - +
97A LEU* 1.3 62.5 + - - +
98A LEU 3.1 2.0 - - - -
99A ALA* 3.2 26.1 + - + +
102A HIS* 3.7 9.4 - - - +
9B PRO* 4.7 10.8 - - + -
10B LEU* 3.6 46.0 - - + +
12B PRO* 3.8 8.7 - - + -
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Residues in contact with LEU 97 (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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94A LEU* 3.0 21.4 + - + +
96A MSE 1.3 77.1 - - - +
98A LEU* 1.3 60.3 + - + +
99A ALA 3.4 5.5 + - - +
102A HIS* 3.3 41.3 - - + +
104A ALA* 4.6 3.8 - - + -
106A GLN* 3.9 8.3 + - + +
107A ARG 3.9 13.7 + - - -
12B PRO* 3.6 13.3 - - + +
16B ASP* 3.8 11.2 - - + +
17B LEU* 3.7 49.8 - - + +
20B LEU* 3.7 29.4 - - + -
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Residues in contact with LEU 98 (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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33A LEU* 3.8 26.2 - - + +
36A ALA* 4.2 22.7 - - + -
37A ALA* 4.4 10.1 - - + +
40A ARG* 6.0 0.2 - - - -
42A VAL* 3.7 20.8 - - + +
43A ASP* 4.2 1.9 - - - +
78A VAL* 4.3 13.5 - - + -
94A LEU* 6.4 0.9 - - + -
95A GLY* 3.1 14.6 + - - +
96A MSE 3.1 1.4 - - - -
97A LEU* 1.3 80.5 - - + +
99A ALA* 1.3 63.2 + - - +
100A ASP 3.5 0.7 + - - -
106A GLN 4.5 0.2 - - - -
107A ARG* 3.2 38.3 - - + +
110A LEU* 3.8 28.3 - - + -
20B LEU* 4.6 7.0 - - + -
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Residues in contact with ALA 99 (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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42A VAL* 3.6 9.8 - - + +
43A ASP* 3.5 7.9 - - - +
46A LEU* 4.1 23.6 - - + -
96A MSE 3.2 23.6 + - + +
97A LEU 3.9 1.7 - - - +
98A LEU* 1.3 78.4 - - - +
100A ASP* 1.3 64.4 + - - +
101A GLY 3.2 3.8 - - - +
102A HIS* 3.1 21.7 + - + +
105A GLN* 5.7 1.2 - - - -
107A ARG* 4.5 3.0 + - - +
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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