Contacts of the strand formed by residues 44 - 51 (chain B) in PDB entry 43C9
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 GLY 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A PHE* 6.1 2.7 - - - -
38B ARG* 3.5 1.4 - - - +
39B GLN* 3.3 9.5 - - - -
40B SER* 2.8 41.2 + - - -
41B PRO 4.2 2.8 + - - -
42B GLY 3.5 2.4 - - - -
43B LYS* 1.3 74.9 - - - +
45B LEU* 1.3 60.5 + - - -
46B GLU* 3.8 3.1 + - - +
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Residues in contact with LEU 45 (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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44A PRO* 4.6 7.4 - - + -
87A PHE* 3.6 53.1 - - + -
98A PHE* 3.5 47.2 + - + +
99A GLY 5.5 0.2 - - - +
37B VAL* 3.7 25.4 - - + -
38B ARG 3.5 1.3 - - - -
39B GLN* 3.8 29.4 - - + +
43B LYS 3.9 1.8 + - - +
44B GLY* 1.3 73.1 - - - -
46B GLU* 1.3 63.5 + - - +
91B TYR* 5.6 0.7 - - + -
103B TRP* 4.3 13.0 - - + -
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PHE* 3.9 5.1 - - - -
37B VAL* 3.3 3.5 - - - +
38B ARG* 2.7 78.3 + - + +
43B LYS* 3.4 40.9 - - - +
44B GLY 4.1 3.6 - - - +
45B LEU* 1.3 79.6 - - - +
47B TRP* 1.3 64.9 + - - +
48B LEU* 3.6 5.8 + - + +
60B ASN* 5.9 1.6 - - - +
63B LEU* 5.8 1.9 - - + +
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Residues in contact with TRP 47 (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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89A GLN* 3.7 19.5 - - - -
94A ALA* 4.1 10.5 - - + -
95A PRO* 3.5 31.4 - - + -
96A ARG* 3.3 37.4 - - + +
97A THR* 4.7 2.1 - - - +
98A PHE* 3.7 9.3 - - + -
35B HIS* 3.1 24.4 + - - -
36B TRP 4.1 3.6 - - - -
37B VAL* 4.0 14.1 - - + -
46B GLU* 1.3 72.5 - - - +
48B LEU* 1.3 60.5 + - - +
49B GLY* 3.5 32.3 + - - -
50B MET* 3.6 20.0 - - + -
58B GLU* 3.9 20.4 - - + -
59B TYR 3.9 22.0 - - - -
60B ASN* 2.9 31.1 + - - +
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Residues in contact with LEU 48 (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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36B TRP* 2.8 23.4 + - + +
37B VAL* 4.1 13.7 - - - +
38B ARG* 4.1 23.3 - - + +
46B GLU* 4.1 11.4 - - + +
47B TRP* 1.3 77.3 - - - +
49B GLY* 1.3 56.8 + - - +
59B TYR* 3.8 0.9 - - - +
60B ASN* 3.2 23.0 + - - +
63B LEU* 3.5 25.8 - - + -
67B LEU* 3.3 26.3 - - + +
69B ILE* 4.6 1.1 - - - -
80B LEU* 3.7 29.8 - - + -
82B MET* 5.5 2.9 - - - -
90B TYR* 4.0 20.9 - - + -
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Residues in contact with GLY 49 (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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35B HIS* 3.4 1.4 - - - -
36B TRP 3.0 20.9 + - - +
47B TRP* 3.5 20.6 - - - -
48B LEU* 1.3 81.1 - - - +
50B MET* 1.3 63.6 + - - +
58B GLU 3.0 16.2 - - - -
69B ILE* 3.6 13.6 - - - +
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Residues in contact with MET 50 (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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96A ARG* 3.6 32.1 - - - +
33B ASN* 4.1 14.6 - - + +
34B VAL 3.2 14.1 - - - +
35B HIS* 3.7 28.0 - - + +
36B TRP* 4.7 0.4 - - - +
47B TRP* 3.6 12.8 - - + -
49B GLY* 1.3 75.3 - - - +
51B ILE* 1.3 61.3 + - - +
52B TRP* 3.5 41.1 - - + +
56B SER 3.9 0.2 - - - +
57B ILE* 3.3 7.1 - - - +
58B GLU* 2.9 50.9 + - + +
69B ILE* 3.6 8.1 - - - +
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Residues in contact with ILE 51 (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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32B TYR 4.6 0.3 - - - +
33B ASN* 3.8 0.3 - - - -
34B VAL* 2.9 35.3 + - + +
50B MET* 1.3 76.5 - - - +
52B TRP* 1.3 68.7 + - - +
55B GLY* 3.5 25.4 - - - +
56B SER 3.2 3.6 - - - -
57B ILE* 3.9 15.0 - - + -
69B ILE* 4.1 7.2 - - + -
70B SER* 4.0 13.5 - - - -
71B LYS* 3.5 41.7 - - + +
78B ILE* 4.0 24.5 - - + -
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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