Contacts of the strand formed by residues 44 - 50 (chain F) in PDB entry 2CHS
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 GLN 44 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D GLY* 3.7 13.9 - - - -
44D GLN* 5.0 5.2 - - - +
46D LEU* 5.3 3.5 - - - +
92D MET* 3.9 28.9 - - - +
94D THR* 2.6 39.7 + - - +
44E GLN* 5.1 4.7 - - - +
42F VAL* 3.4 9.1 - - - +
43F VAL* 1.3 84.2 - - + +
45F MET* 1.3 63.8 + - - +
46F LEU* 4.9 11.2 - - + +
72F PRO* 3.5 18.6 - - + +
92F MET 4.2 0.6 - - - +
93F MET* 3.8 0.5 - - - -
94F THR* 3.0 40.1 + - - +
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Residues in contact with MET 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D MET* 4.5 2.9 - - - +
28F LEU* 3.7 27.4 - - + -
42F VAL* 4.4 2.0 - - + -
44F GLN* 1.3 75.9 - - - +
46F LEU* 1.3 69.8 + - - +
47F LEU* 4.5 7.9 - - + -
62F VAL* 3.9 20.0 - - + -
68F TRP* 3.8 13.0 - - + -
71F VAL* 3.8 19.5 - - + -
72F PRO 3.1 4.7 + - - +
73F VAL* 3.3 25.8 - - + -
74F THR 3.3 21.1 + - - -
91F VAL* 3.8 20.6 - - + -
92F MET 3.6 3.8 - - - -
93F MET* 3.7 24.5 - - + -
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Residues in contact with LEU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 4.1 20.2 - - + -
76D MET* 4.8 3.8 - - + -
92D MET* 4.8 7.6 - - + -
44E GLN* 4.9 6.5 - - - +
46E LEU* 3.8 35.7 - - + -
44F GLN* 4.9 9.4 - - + +
45F MET* 1.3 84.5 - - - +
47F LEU* 1.3 62.5 + - - +
74F THR* 3.4 28.3 - - + +
76F MET* 4.1 22.9 - - + -
90F ARG 3.8 0.3 - - - +
91F VAL* 3.3 4.9 - - - +
92F MET* 3.0 44.0 + - + +
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Residues in contact with LEU 47 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24F THR* 3.9 27.1 - - + -
27F LEU* 5.6 1.3 - - + -
28F LEU* 5.4 2.5 - - + -
45F MET* 4.5 5.8 - - + -
46F LEU* 1.3 78.7 - - - +
48F SER* 1.3 58.4 + - - +
58F PRO* 4.2 18.4 - - + -
59F ALA* 3.7 32.1 - - + -
62F VAL* 4.2 15.3 - - + -
73F VAL* 4.3 11.9 - - + -
74F THR 3.0 7.0 + - - +
75F CYS* 3.0 32.9 - - - +
76F MET* 3.0 6.1 + - - +
89F ILE* 4.3 9.2 - - + -
90F ARG 3.2 4.0 - - - -
91F VAL* 4.1 22.4 - - + -
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Residues in contact with SER 48 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79D MET* 5.3 1.6 - - - -
74E THR* 5.1 0.7 + - - -
75E CYS 4.8 1.4 + - - -
47F LEU* 1.3 73.1 - - - +
49F ALA* 1.3 60.4 - - - +
58F PRO* 5.4 0.9 - - - -
76F MET* 3.2 39.7 - - - +
78F GLU* 4.0 19.6 + - - +
89F ILE* 3.3 8.3 - - - +
90F ARG* 2.8 56.3 + - - +
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Residues in contact with ALA 49 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79D MET* 3.8 33.7 - - + +
48F SER* 1.3 76.4 - - - +
50F THR* 1.3 68.5 + - - +
53F LEU* 3.9 20.0 - - + -
58F PRO* 4.5 8.1 - - + -
76F MET 3.4 4.2 + - - -
77F GLN* 3.7 8.0 - - - +
78F GLU* 3.0 21.7 + - - -
88F CYS 3.5 6.7 - - - -
89F ILE* 4.6 1.1 - - + -
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Residues in contact with THR 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D MET* 6.1 0.2 - - - +
57E PHE* 6.2 1.1 - - + -
49F ALA* 1.3 79.5 - - - +
51F PRO* 1.3 68.5 - - + +
52F ASP* 2.6 33.1 + - - -
53F LEU* 3.2 17.3 + - - +
78F GLU* 4.1 10.2 - - + +
79F MET 5.1 2.5 - - - +
85F LEU 3.4 25.1 - - - +
86F LYS* 4.7 4.5 - - + +
87F LYS* 3.2 2.4 + - - -
88F CYS* 3.1 26.9 + - + +
90F ARG* 3.8 21.1 - - - +
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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