Contacts of the strand formed by residues 12 - 21 (chain C) in PDB entry 1XS2
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 ALA 12 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C ILE* 3.7 4.8 - - - +
11C GLU* 1.3 82.8 - - + +
13C ALA* 1.3 63.5 + - - +
43C LEU* 3.6 1.6 - - - -
44C HIS* 2.9 45.3 + - + +
83C LEU* 3.8 4.9 - - - -
372C GLU* 4.5 6.3 - - - +
373C HIS 3.5 9.4 - - - +
374C ARG* 3.7 30.5 - - + +
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Residues in contact with ALA 13 (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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12C ALA* 1.3 77.8 - - - +
14C GLU* 1.3 63.4 + - - +
41C LEU* 4.4 3.4 - - + -
42C ILE 3.1 11.9 - - - +
43C LEU* 3.7 19.1 - - + -
44C HIS* 4.6 0.4 - - - -
79C LEU* 4.3 24.2 - - + -
83C LEU* 4.4 9.2 - - + -
371C GLU 4.1 0.2 - - - +
372C GLU* 3.6 3.2 - - - +
373C HIS* 2.9 35.3 + - + +
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Residues in contact with GLU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ALA* 1.3 77.3 - - - +
15C ILE* 1.3 61.3 - - - +
16C VAL* 4.0 20.4 + - + +
40C LEU 3.8 0.3 - - - +
41C LEU* 3.5 7.7 - - - +
42C ILE* 3.0 38.3 + - + +
44C HIS* 2.7 29.2 + - + +
360C ARG* 2.9 30.3 + - - -
370C GLN* 6.0 0.2 + - - -
371C GLU 3.3 9.2 - - - +
372C GLU* 3.8 27.1 - - + +
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Residues in contact with ILE 15 (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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13C ALA 4.3 0.6 + - - -
14C GLU* 1.3 75.0 - - - +
16C VAL* 1.3 63.4 + - - +
17C VAL* 4.5 9.2 - - + -
39C PRO* 6.0 0.2 - - + -
40C LEU 3.5 8.5 - - - +
41C LEU* 4.0 14.8 - - + -
71C LEU* 3.9 36.1 - - + +
74C LEU* 4.2 23.8 - - + -
75C ARG* 4.7 3.1 - - - +
79C LEU* 4.1 20.9 - - + -
109C MET* 5.7 0.9 - - + -
369C ALA 3.9 0.9 - - - +
370C GLN* 3.2 5.4 - - - -
371C GLU* 3.0 61.6 + - + +
373C HIS* 5.0 0.4 - - + -
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Residues in contact with VAL 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLU* 4.1 25.1 - - + +
15C ILE* 1.3 79.6 - - - +
17C VAL* 1.3 62.6 + - - +
18C ALA 3.9 0.3 + - - -
38C VAL 3.6 2.1 - - - +
40C LEU* 2.8 45.9 + - + +
42C ILE* 4.2 15.9 - - + -
360C ARG* 6.0 1.3 - - - +
363C LEU* 4.2 21.8 - - + -
367C THR* 3.7 25.6 - - + +
369C ALA 3.6 8.1 - - - +
370C GLN* 4.6 13.0 - - + +
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Residues in contact with VAL 17 (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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15C ILE* 4.5 9.0 - - + -
16C VAL* 1.3 75.2 - - - +
18C ALA* 1.3 59.3 + - - +
37C VAL* 3.3 33.9 - - + -
38C VAL 3.5 7.0 - - - +
39C PRO* 4.4 9.2 - - + -
67C ILE* 5.3 3.8 - - + -
71C LEU* 4.1 26.2 - - + -
367C THR* 3.6 3.1 - - - -
368C GLU* 2.9 36.9 + - + +
369C ALA* 3.0 31.2 + - + +
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Residues in contact with ALA 18 (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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16C VAL 3.9 0.9 + - - +
17C VAL* 1.3 77.0 - - - +
19C ARG* 1.3 62.1 + - - +
20C LEU* 4.1 0.9 - - + -
37C VAL* 3.3 8.0 - - - +
38C VAL* 2.8 39.7 + - + +
40C LEU* 5.6 0.2 - - + -
334C LEU* 4.3 12.6 - - + -
363C LEU* 3.8 28.3 - - + -
366C VAL* 3.3 19.5 - - + +
367C THR* 4.2 0.9 - - - +
368C GLU* 5.1 1.6 - - - -
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Residues in contact with ARG 19 (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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18C ALA* 1.3 75.0 - - - +
20C LEU* 1.3 60.4 + - - +
21C PRO* 3.9 2.1 - - - +
34C THR* 6.1 0.4 - - - +
35C HIS* 3.6 45.9 + - + +
36C LYS 3.6 5.6 - - - +
37C VAL* 3.6 26.1 - - + +
366C VAL* 2.9 34.8 + - - +
368C GLU* 3.1 35.4 + - + +
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Residues in contact with LEU 20 (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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18C ALA* 5.4 0.9 - - + -
19C ARG* 1.3 72.8 - - - +
21C PRO* 1.3 74.8 - - + +
22C LEU 3.6 0.2 + - - -
35C HIS* 3.4 3.6 - - - -
36C LYS 2.9 34.5 + - - +
38C VAL* 4.3 14.4 - - + -
301C SER* 4.3 5.8 - - - -
330C TRP* 3.6 49.4 - - + -
332C ARG 4.1 8.5 - - - +
333C ASP* 4.7 0.9 - - - +
334C LEU* 3.6 41.1 - - + -
362C PHE* 3.9 17.7 - - + -
366C VAL* 4.2 9.2 - - + -
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Residues in contact with PRO 21 (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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19C ARG 3.9 6.3 - - - +
20C LEU* 1.3 93.7 - - + +
22C LEU* 1.3 67.0 + - - +
34C THR 3.7 9.0 - - - +
35C HIS* 3.8 20.8 - - + +
329C TYR 4.4 0.9 - - - +
330C TRP* 3.4 19.5 - - - +
331C GLU* 4.5 19.0 + - + +
332C ARG 5.8 0.9 - - - +
362C PHE* 5.4 5.2 - - + -
366C VAL* 4.7 9.2 - - + -
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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