Contacts of the strand formed by residues 26 - 34 (chain X) in PDB entry 2W6C
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 HIS 26 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X ARG* 3.1 52.7 + - + +
20X VAL 3.2 9.5 - - - +
21X PRO* 3.7 24.5 - - + +
22X VAL* 4.0 2.0 - - - -
24X SER 5.8 0.8 - - - -
25X SER* 1.3 113.1 + - - +
27X ILE* 1.3 71.1 + - - +
103X SER* 4.0 10.7 + - - +
137X TYR* 4.7 1.4 - - - -
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Residues in contact with ILE 27 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X ARG* 3.4 8.1 - - - +
20X VAL* 2.9 38.6 + - + -
22X VAL* 3.8 10.1 - - + -
26X HIS* 1.3 84.2 - - - +
28X SER* 1.3 68.5 + - - +
100X TRP* 4.1 9.9 - - + -
101X VAL 3.4 8.7 - - - +
102X PRO* 4.2 15.5 - - + -
103X SER* 4.1 11.0 - - - +
133X LYS* 3.8 37.9 - - + +
136X ALA* 4.1 15.7 - - + -
137X TYR* 4.0 24.9 - - + -
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Residues in contact with SER 28 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X GLU* 3.9 20.9 + - - +
6X LEU* 3.5 28.0 - - - +
18X THR 3.7 3.8 - - - -
19X ARG* 5.8 0.2 - - - +
27X ILE* 1.3 83.3 - - - +
29X ALA* 1.3 61.1 + - - +
30X PHE* 4.0 18.6 - - - -
100X TRP* 3.5 4.2 - - - -
101X VAL* 2.9 38.0 + - - +
102X PRO 4.5 2.9 + - - -
103X SER* 4.6 1.6 - - - -
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Residues in contact with ALA 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X GLY* 3.2 4.5 - - - -
18X THR* 3.0 32.3 + - + +
20X VAL* 4.0 21.1 - - + -
28X SER* 1.3 76.2 - - - +
30X PHE* 1.3 63.2 + - - +
31X LEU* 3.9 26.7 - - + -
60X ALA 3.6 2.8 - - - +
99X ILE 3.3 5.2 - - - -
100X TRP* 4.0 17.7 - - + +
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Residues in contact with PHE 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X GLU 3.9 15.0 - - - -
6X LEU* 3.4 24.2 - - - -
8X VAL* 3.6 26.0 - - + -
15X VAL* 3.1 28.7 - - + -
17X GLY* 3.5 12.1 - - - -
28X SER* 4.0 19.7 - - - -
29X ALA* 1.3 73.7 - - - +
31X LEU* 1.3 60.6 + - - +
33X ILE* 3.8 22.0 - - + +
60X ALA* 3.5 7.6 - - + -
98X ASN* 3.5 3.6 - - - -
99X ILE* 2.9 38.7 + - + +
101X VAL* 4.0 13.5 - - + -
105X ARG* 4.9 1.1 - - - -
187X PHE* 3.7 21.3 - + + -
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Residues in contact with LEU 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X THR* 4.8 3.6 - - + -
29X ALA* 3.9 27.1 - - + -
30X PHE* 1.3 78.4 - - - +
32X GLY* 1.3 65.4 + - - +
33X ILE 3.4 0.7 - - - -
59X ASN 4.4 0.7 - - - +
60X ALA* 2.8 34.2 + - - +
61X SER 3.9 17.3 - - - +
62X THR* 3.5 19.8 - - - +
63X TYR* 3.9 31.4 - - + +
98X ASN* 3.7 23.8 - - + +
99X ILE 4.7 0.9 - - - +
100X TRP* 4.1 12.3 - - + +
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Residues in contact with GLY 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X LEU* 1.3 73.5 - - - +
33X ILE* 1.3 61.9 + - - +
58X TRP* 3.2 20.0 + - - -
59X ASN 5.0 0.3 - - - +
62X THR 4.1 3.6 - - - -
64X PRO* 3.8 31.1 - - - +
96X TYR* 3.3 14.8 - - - -
97X LEU 3.2 4.3 + - - -
98X ASN* 3.0 13.3 + - - -
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Residues in contact with ILE 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15X VAL* 4.2 22.7 - - + -
30X PHE* 3.8 29.6 - - + +
32X GLY* 1.3 76.5 - - - +
34X PRO* 1.4 81.5 - - + +
54X TRP* 5.1 2.7 - - + -
58X TRP* 4.4 1.6 - - + +
60X ALA* 4.1 17.5 - - + -
96X TYR* 3.3 1.4 - - - -
97X LEU* 2.8 39.3 + - + +
99X ILE* 3.9 22.7 - - + -
179X TRP* 4.0 23.8 - - + -
187X PHE* 4.3 7.6 - - + -
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Residues in contact with PRO 34 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32X GLY 3.8 1.3 - - - +
33X ILE* 1.4 99.0 - - + +
35X PHE* 1.3 59.1 + - - +
36X ALA 4.5 4.3 - - - +
51X LYS* 3.8 39.0 - - + +
54X TRP* 3.9 19.2 - - + -
58X TRP* 3.6 33.9 - - + -
95X LEU 3.7 2.9 - - - +
96X TYR* 3.5 23.5 - - + +
179X TRP* 4.4 7.6 + - - -
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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