Contacts of the strand formed by residues 25 - 32 (chain C) in PDB entry 6XHU
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 THR 25 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C THR* 3.3 3.3 - - - +
22C CYS 2.9 29.5 + - - -
24C THR* 1.3 88.0 - - - +
26C THR* 1.3 67.1 + - - +
27C LEU* 4.6 6.7 - - + -
41C HIS* 4.4 4.9 - - + +
42C VAL* 3.3 40.2 + - + +
44C CYS 2.9 23.2 + - - +
45C THR* 4.5 0.9 - - - -
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Residues in contact with THR 26 (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 GLN* 3.5 33.8 - - + +
20C VAL 3.3 4.0 - - - +
21C THR* 2.4 28.2 + - - +
24C THR 3.7 5.5 + - - -
25C THR* 1.3 76.1 - - - +
27C LEU* 1.3 69.2 + - - +
119C ASN* 3.7 19.7 - - - +
143C GLY* 4.6 11.6 - - - -
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLN* 3.7 4.6 - - - -
20C VAL* 2.9 32.6 + - + +
25C THR* 4.6 6.5 - - + -
26C THR* 1.3 79.0 - - - +
28C ASN* 1.3 92.5 + - - +
38C CYS* 3.8 9.2 - - + -
39C PRO* 3.3 24.5 - - + -
41C HIS* 4.2 12.8 - - + +
42C VAL* 3.8 39.9 - - + +
119C ASN 5.5 1.6 - - - +
120C GLY 5.3 0.9 - - - -
143C GLY* 4.5 9.9 - - - +
145C CYS* 3.6 28.3 - - + +
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Residues in contact with ASN 28 (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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17C MET* 3.9 12.1 - - + -
18C VAL 3.5 4.7 - - - +
20C VAL* 4.7 0.4 - - - -
27C LEU* 1.3 97.2 - - - +
29C GLY* 1.3 59.4 + - - +
38C CYS* 3.6 3.3 - - - +
117C CYS* 3.1 37.5 + - - +
119C ASN 3.5 3.3 + - - -
120C GLY* 2.7 32.9 + - - -
143C GLY 3.1 14.5 + - - -
144C SER 3.4 6.1 + - - -
145C CYS 3.1 21.2 + - - +
146C GLY* 3.4 22.7 - - - -
147C SER* 3.9 0.4 + - - -
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Residues in contact with GLY 29 (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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17C MET* 3.4 13.4 - - - +
18C VAL* 2.9 44.9 + - - -
20C VAL* 4.2 5.2 - - - +
27C LEU 4.0 0.2 + - - -
28C ASN* 1.3 74.3 - - - +
30C LEU* 1.3 59.6 + - - -
36C VAL* 4.3 0.4 - - - -
37C TYR 3.2 13.2 - - - -
38C CYS* 4.0 6.1 - - - -
146C GLY 4.9 2.5 - - - -
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Residues in contact with LEU 30 (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 VAL* 5.1 0.4 - - + -
16C CYS* 3.6 27.8 - - + +
17C MET* 4.2 14.6 - - - -
29C GLY* 1.3 74.2 - - - -
31C TRP* 1.3 58.1 + - - +
32C LEU* 3.7 26.0 - - + -
36C VAL* 3.3 2.8 - - - +
37C TYR* 2.7 50.4 + - + +
148C VAL* 4.3 16.6 - - + -
159C PHE* 3.9 34.5 - - + -
162C MET* 4.4 1.6 - - + -
177C LEU* 3.7 26.2 - - + -
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Residues in contact with TRP 31 (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 GLY 5.1 4.0 - - - -
16C CYS* 2.9 24.4 + - - +
18C VAL* 3.6 26.9 - - + -
29C GLY 4.1 0.2 - - - -
30C LEU* 1.3 70.9 - - - +
32C LEU* 1.3 59.6 + - - +
33C ASP 3.0 23.4 + - - -
35C VAL 3.5 10.8 - - - -
36C VAL* 3.9 16.6 - - + -
70C ALA* 3.4 22.7 - - + -
73C VAL* 5.6 2.2 - - + -
75C LEU* 3.6 30.7 - - + -
91C VAL* 3.8 6.3 - - + +
93C THR* 3.1 27.8 + - + -
94C ALA 3.9 2.7 - - - -
95C ASN* 2.8 61.2 + - + -
96C PRO* 4.3 8.5 - - + -
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Residues in contact with LEU 32 (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 CYS* 3.8 21.8 - - + -
30C LEU* 3.7 30.0 + - + -
31C TRP* 1.3 79.9 - - - +
33C ASP* 1.3 74.1 + - - +
35C VAL* 3.1 23.3 + - - +
37C TYR* 4.3 9.2 + - + -
98C THR* 4.0 3.4 - - + -
99C PRO* 4.1 8.7 - - + -
101C TYR* 3.8 36.8 + - + +
103C PHE* 3.7 27.6 - - + -
159C PHE* 4.0 15.9 - - + -
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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