Contacts of the strand formed by residues 11 - 18 (chain B) in PDB entry 1XFS
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 ASP 11 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ARG* 2.7 40.1 + - - -
6B ILE* 3.6 21.7 - - + +
7B ASP 2.8 33.6 + - - +
8B ALA* 4.0 14.6 - - - +
10B LEU* 1.3 83.8 - - - +
12B LEU* 1.3 70.0 - - - +
13B MSE 4.3 0.7 + - - -
132B CYS* 3.8 17.9 - - - -
133B ALA 3.3 2.5 - - - -
134B MSE 3.3 15.9 - - - +
141B ARG* 4.8 0.2 - - - +
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Residues in contact with LEU 12 (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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11B ASP* 1.3 80.4 - - - +
13B MSE 1.3 62.1 + - - +
132B CYS* 3.2 5.9 - - - -
133B ALA* 2.8 34.8 + - + +
135B HIS* 3.7 24.7 - - + -
141B ARG* 3.8 17.9 - - + +
144B HIS* 4.2 9.9 - - + +
145B GLU* 3.6 59.2 - - + +
153B TRP* 3.3 18.4 - - + -
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Residues in contact with MSE 13 (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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6B ILE* 3.3 44.6 - - + +
11B ASP 4.3 0.6 + - - -
12B LEU* 1.3 77.3 - - - +
14B LEU* 1.3 63.3 + - - +
15B LYS* 3.4 39.7 - - + +
130B THR* 4.3 11.0 - - - -
131B ALA 3.4 7.9 - - - +
132B CYS* 4.2 11.7 - - + -
153B TRP* 3.7 5.3 - - - -
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Residues in contact with LEU 14 (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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13B MSE 1.3 76.8 - - - +
15B LYS* 1.3 65.3 + - - +
16B ARG* 4.2 17.9 - - + -
129B TYR* 3.6 7.1 - - + +
130B THR* 3.5 3.3 - - - +
131B ALA* 2.8 34.3 + - + +
153B TRP* 3.5 66.2 - - + +
154B GLY* 4.2 13.7 - - - +
157B ILE* 3.5 20.0 - - + -
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Residues in contact with LYS 15 (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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13B MSE 3.4 40.5 - - + +
14B LEU* 1.3 80.0 - - - +
16B ARG* 1.3 70.2 + - - +
128B ARG* 3.3 38.1 - - - +
129B TYR 3.4 5.8 - - - +
130B THR* 3.6 15.1 - - + +
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Residues in contact with ARG 16 (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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14B LEU* 4.2 20.4 - - + -
15B LYS* 1.3 84.2 - - - +
17B GLU* 1.3 71.4 + - - +
18B LEU* 4.9 2.5 - - + -
128B ARG* 3.8 1.5 - - - +
129B TYR* 2.8 42.1 + - + +
154B GLY* 2.8 23.3 + - - -
157B ILE* 3.4 30.8 - - + +
158B THR* 2.8 42.4 + - - +
161B GLU* 4.5 13.6 + - - -
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Residues in contact with GLU 17 (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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16B ARG* 1.3 79.2 + - - +
18B LEU* 1.3 66.1 + - - +
19B ALA 4.0 1.4 + - - -
123B THR* 3.8 25.8 + - - +
127B THR 3.8 2.4 + - - +
128B ARG* 3.6 36.0 + - - +
161B GLU* 4.2 6.2 - - - +
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Residues in contact with LEU 18 (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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16B ARG* 4.6 5.2 - - + +
17B GLU* 1.3 76.8 - - - +
19B ALA* 1.3 59.0 + - - +
20B VAL* 2.8 15.5 + - + +
25B VAL* 3.9 36.3 - - + -
126B GLY* 3.2 1.7 - - - -
127B THR* 2.8 39.7 + - - +
129B TYR* 4.2 21.1 - - + -
157B ILE* 3.8 24.2 - - + +
160B LEU* 4.4 18.8 - - + -
161B GLU* 3.6 33.9 - - + +
164B LEU* 5.4 2.2 - - + -
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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