Contacts of the strand formed by residues 22 - 31 (chain B) in PDB entry 3H9R
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 22 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ASN* 5.3 5.7 + - - +
20B GLY 4.0 0.4 + - - -
21B GLN* 1.3 71.4 - - - +
23B CYS* 1.3 62.1 + - - +
24B VAL* 3.7 1.9 + - + -
48B LYS* 3.8 30.7 - - + -
49B PHE 3.4 10.1 - - - +
50B MET* 3.7 23.0 - - - +
107B LEU* 3.3 7.3 - - - -
108B GLU* 2.8 64.0 + - + +
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Residues in contact with CYS 23 (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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17B PRO* 3.7 34.1 - - - -
21B GLN 4.4 3.8 - - - -
22B THR* 1.3 71.6 - - - +
24B VAL* 1.3 60.0 + - - +
25B VAL* 3.9 1.9 + - + -
47B PHE 3.5 1.9 - - - +
48B LYS* 3.2 5.4 - - - -
49B PHE* 2.8 53.4 + - + +
51B LEU* 4.0 21.3 - - - -
64B VAL* 4.1 7.6 - - + -
104B LEU* 4.0 11.4 - - + -
106B LYS 3.9 4.5 - - - -
107B LEU* 3.8 6.3 - - - -
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Residues in contact with VAL 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B THR* 4.4 5.6 - - + +
23B CYS* 1.3 74.7 - - - +
25B VAL* 1.3 63.4 + - - +
46B PRO* 3.6 28.7 - - + -
47B PHE 3.4 5.6 - - - +
48B LYS* 4.1 17.3 - - + +
104B LEU* 3.9 0.5 - - - -
105B LEU* 2.9 34.9 + - + +
106B LYS* 2.9 32.9 + - + +
108B GLU* 3.6 31.2 - - + +
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Residues in contact with VAL 25 (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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23B CYS* 4.4 11.0 - - + -
24B VAL* 1.3 80.7 - - - +
26B HIS* 1.3 64.6 + - - +
27B TYR* 4.4 0.7 - - + -
46B PRO* 3.6 4.9 - - - +
47B PHE* 2.8 49.1 + - + +
49B PHE* 4.6 8.5 - - + -
60B TRP* 3.7 33.4 - - + -
64B VAL* 4.8 3.8 - - + -
102B VAL* 4.0 16.6 - - + -
103B GLU 3.1 13.5 - - - +
104B LEU* 4.0 18.6 - - + -
105B LEU* 4.3 4.7 - - - +
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Residues in contact with HIS 26 (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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25B VAL* 1.3 74.2 + - - +
27B TYR* 1.3 60.5 + - - +
40B SER* 2.8 45.4 + - - -
41B ARG* 3.6 44.5 + - + +
44B ASN* 4.2 13.9 + - - -
45B LYS 3.9 4.5 - - - -
46B PRO* 3.8 26.3 - - - +
101B ASP 3.7 0.5 - - - +
102B VAL* 3.3 4.2 - - - +
103B GLU* 2.8 35.1 + - + -
105B LEU* 4.0 22.7 - - + +
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Residues in contact with TYR 27 (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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199A LEU* 3.3 26.4 + - + +
200A VAL* 4.4 3.1 + - - +
25B VAL* 4.4 0.2 - - + -
26B HIS* 1.3 76.5 - - - +
28B THR* 1.3 63.3 + - - +
29B GLY 4.0 9.2 - - - -
38B ASP* 2.5 43.5 + - + -
39B SER* 3.1 5.0 + - - -
40B SER* 2.9 50.1 + - - -
41B ARG* 4.1 3.1 + - - +
43B ARG* 2.9 20.7 + - - -
47B PHE* 3.6 35.4 - + + -
60B TRP* 3.5 33.0 - + + -
100B PHE* 4.5 3.4 - + + -
101B ASP 3.1 8.7 - - - +
102B VAL* 4.5 2.5 - - + -
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Residues in contact with THR 28 (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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27B TYR* 1.3 72.4 + - - +
29B GLY* 1.3 65.5 + - - +
30B MET* 3.9 17.6 - - + +
36B LYS* 3.9 28.3 - - + -
38B ASP 3.6 2.9 - - - -
39B SER* 2.7 18.5 + - - -
41B ARG* 4.1 13.0 + - - +
99B VAL 3.8 1.4 - - - +
100B PHE* 3.3 2.7 - - - -
101B ASP* 2.7 49.8 + - - +
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Residues in contact with GLY 29 (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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27B TYR* 4.0 4.0 - - - -
28B THR* 1.3 74.1 - - - +
30B MET* 1.3 63.9 + - - +
36B LYS* 3.5 2.4 - - - +
37B PHE* 3.1 32.0 + - - -
38B ASP 2.8 19.2 + - - +
100B PHE* 3.4 29.8 - - - -
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Residues in contact with MET 30 (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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28B THR* 3.9 30.1 - - + +
29B GLY* 1.3 77.5 - - - +
31B LEU* 1.3 67.5 + - - +
34B GLY* 3.5 28.3 - - - +
35B LYS 3.3 7.2 - - - +
36B LYS* 3.9 9.2 - - + -
37B PHE* 3.5 12.3 - - - -
74B LYS* 4.9 8.5 - - - +
98B LEU* 3.6 6.1 - - - +
99B VAL* 2.8 50.5 + - + +
101B ASP* 4.4 15.7 - - + -
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Residues in contact with LEU 31 (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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30B MET* 1.3 79.8 - - - +
32B GLU* 1.3 61.2 + - - +
33B ASP* 3.3 18.4 - - - +
34B GLY* 2.9 18.4 + - - -
35B LYS* 2.9 36.2 + - + +
37B PHE* 3.9 15.7 - - + -
91B ILE 4.5 5.6 - - - +
92B ILE* 4.0 10.1 - - + -
93B PRO* 3.9 31.9 - - + -
96B ALA* 4.6 3.6 - - + -
97B THR 3.9 3.4 - - - -
98B LEU* 3.5 24.0 - - + -
99B VAL* 4.4 7.2 - - - +
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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