Contacts of the strand formed by residues 51 - 57 (chain F) in PDB entry 6H25
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 51 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44F GLY* 5.7 0.9 - - - -
49F ALA* 3.4 3.7 - - - +
50F LYS* 1.3 80.7 - - - +
52F SER* 1.3 61.1 + - - -
65F ALA* 3.2 4.7 - - - +
66F VAL* 2.9 29.1 + - - +
168F ALA* 4.1 8.1 - - - -
171F ASP* 4.5 4.5 - - - -
172F ALA* 3.8 23.6 - - - +
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Residues in contact with SER 52 (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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43F ALA* 3.3 5.5 - - - +
44F GLY* 2.6 32.6 + - - +
45F LEU* 2.7 33.0 + - - -
46F LEU* 2.8 37.3 + - - +
49F ALA* 4.9 0.7 - - - -
51F GLY* 1.3 75.8 - - - -
53F ALA* 1.3 61.8 + - - +
63F LEU* 5.5 0.7 - - - -
64F CYS 3.2 11.9 - - - -
65F ALA* 4.3 0.4 - - - -
168F ALA* 3.9 8.3 + - - +
171F ASP* 4.0 2.6 + - - +
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Residues in contact with ALA 53 (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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42F ARG 3.5 9.2 - - - +
43F ALA* 4.5 3.4 - - + -
45F LEU* 5.4 2.9 - - - +
52F SER* 1.3 77.4 - - - +
54F TYR* 1.3 62.0 + - - +
63F LEU* 3.5 6.4 - - - +
64F CYS* 2.9 32.4 + - - +
164F ALA* 3.5 29.5 - - - +
167F LEU* 3.9 15.9 - - + -
168F ALA* 3.6 11.2 - - + +
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Residues in contact with TYR 54 (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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40F TYR* 4.5 17.5 - + - -
41F ALA* 3.3 5.2 - - - +
42F ARG* 2.9 37.5 + - + +
45F LEU* 3.8 29.6 - - + -
53F ALA* 1.3 76.6 - - - +
55F LEU* 1.3 61.3 + - - +
56F GLU* 3.7 26.6 + - + -
61F LYS* 3.3 39.4 - - + +
62F VAL 3.7 13.9 - - - -
63F LEU* 4.0 22.7 - - + -
151F LEU* 4.7 15.2 - - + +
167F LEU* 5.9 0.6 - - - +
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Residues in contact with LEU 55 (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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39F VAL* 3.7 22.7 - - + -
40F TYR 3.7 0.7 - - - -
41F ALA* 3.7 23.1 - - + -
53F ALA 4.3 0.4 - - - -
54F TYR* 1.3 76.7 - - - +
56F GLU* 1.3 71.6 + - - +
57F ALA* 5.6 3.6 - - + -
60F THR 3.9 0.7 - - - +
61F LYS* 3.6 2.1 - - - +
62F VAL* 2.9 44.2 + - + +
160F ALA* 3.4 38.1 - - + +
163F THR* 3.8 23.6 - - + -
164F ALA* 3.9 10.5 - - + +
167F LEU* 5.3 2.0 - - + -
255F LEU* 4.6 5.8 - - + -
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Residues in contact with GLU 56 (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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38F PRO 3.8 0.5 - - - +
39F VAL* 3.6 4.5 - - - +
40F TYR* 2.9 63.6 + - + +
54F TYR* 3.7 18.2 + - + +
55F LEU* 1.3 77.3 - - - +
57F ALA* 1.3 64.1 + - - +
58F GLY 4.2 12.2 - - - +
60F THR 3.4 8.1 - - - +
61F LYS* 3.8 30.7 + - + -
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Residues in contact with ALA 57 (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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37F ARG* 4.6 16.5 - - + +
38F PRO 3.5 12.3 - - - +
39F VAL* 4.7 10.8 - - + -
55F LEU* 5.6 4.7 - - + -
56F GLU* 1.3 77.3 - - - +
58F GLY* 1.3 59.6 + - - +
59F GLY 3.0 1.2 + - - -
60F THR* 2.9 39.7 + - + +
160F ALA* 6.0 4.3 - - + -
198F ASP* 5.1 6.1 - - - +
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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