Contacts of the strand formed by residues 60 - 70 (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 THR 60 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55F LEU 3.9 0.7 - - - +
56F GLU* 3.4 4.3 - - - +
57F ALA* 2.9 42.8 + - + -
58F GLY 3.5 0.6 - - - -
59F GLY* 1.3 76.6 + - - +
61F LYS* 1.3 69.4 + - - +
62F VAL* 5.5 0.7 - - + -
150F LEU* 5.8 3.6 - - + -
152F GLU 3.4 9.9 - - - +
153F ASP* 5.5 0.9 - - - -
154F GLY 3.2 2.7 - - - +
155F GLY* 2.8 32.4 + - - +
156F SER* 3.9 21.7 + - - +
157F ALA* 5.2 3.6 - - - -
160F ALA* 4.1 17.5 - - + -
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Residues in contact with LYS 61 (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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41C SER* 3.8 25.2 + - - -
42C ILE* 5.0 9.9 - - + -
54F TYR* 3.3 30.5 - - + +
55F LEU 3.6 4.3 - - - +
56F GLU* 3.8 26.2 + - + +
58F GLY 4.9 7.3 + - - -
59F GLY* 3.9 0.6 + - - -
60F THR* 1.3 79.6 - - - +
62F VAL* 1.3 64.5 + - - +
150F LEU* 4.0 5.4 - - - +
151F LEU* 3.3 31.9 + - + -
152F GLU* 2.6 49.8 + - + +
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Residues in contact with VAL 62 (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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54F TYR* 3.7 7.7 - - - -
55F LEU* 2.9 51.0 + - + +
60F THR* 5.5 0.9 - - + -
61F LYS* 1.3 77.7 - - - +
63F LEU* 1.3 68.8 + - - +
64F CYS* 4.6 4.7 - - - -
100F PHE* 5.5 0.2 - - + -
148F ALA* 5.1 0.4 - - + -
149F LEU 3.4 20.6 - - - +
150F LEU* 4.4 8.3 - - + +
151F LEU* 4.7 2.2 - - - +
157F ALA 6.0 0.2 - - - +
160F ALA* 3.4 36.3 - - + +
161F ALA* 3.9 25.8 - - + +
164F ALA* 3.8 3.8 - - + +
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Residues in contact with LEU 63 (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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88C LEU* 3.7 28.2 - - + +
142C LEU* 4.2 28.0 - - + -
45F LEU* 5.1 8.3 - - + -
46F LEU* 3.8 32.5 - - + -
52F SER* 5.5 0.4 - - - -
53F ALA 3.5 11.9 - - - +
54F TYR* 4.0 23.3 - - + -
62F VAL* 1.3 75.5 - - - +
64F CYS* 1.3 81.9 + - - +
147F SER 4.2 0.2 - - - +
148F ALA* 3.6 0.2 - - - -
149F LEU* 2.9 40.3 + - + +
151F LEU* 5.1 9.4 - - + +
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Residues in contact with CYS 64 (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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52F SER* 3.2 4.2 - - - -
53F ALA 2.9 32.1 + - - +
62F VAL* 4.6 3.1 - - - -
63F LEU* 1.3 86.7 - - - +
65F ALA* 1.3 62.6 + - - +
146F VAL* 5.6 2.2 - - + -
147F SER 3.4 7.2 - - - +
148F ALA* 3.6 23.3 - - - -
161F ALA 3.9 4.0 - - - -
164F ALA* 3.6 26.9 - - + +
165F ALA* 3.4 31.6 - - + -
168F ALA* 3.9 5.2 - - + -
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Residues in contact with ALA 65 (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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88C LEU* 3.7 23.5 - - + +
46F LEU* 3.8 12.1 - - + -
49F ALA* 3.8 19.7 - - + -
51F GLY 3.2 11.4 - - - +
52F SER* 4.2 0.2 - - - +
64F CYS* 1.3 77.8 - - - +
66F VAL* 1.3 67.8 + - - +
67F SER 4.2 0.6 + - - -
145F GLU 3.8 1.2 - - - +
146F VAL* 5.0 0.3 - - - +
147F SER* 3.1 33.3 + - - +
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Residues in contact with VAL 66 (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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49F ALA* 5.1 2.0 - - - -
50F LYS* 3.5 27.5 + - - +
51F GLY 2.9 9.5 + - - +
64F CYS* 6.1 0.2 - - + -
65F ALA* 1.3 79.6 - - - +
67F SER* 1.3 74.7 + - - +
68F GLY* 5.2 1.1 - - - -
144F LEU* 5.0 7.6 - - + -
145F GLU 3.6 9.2 - - - +
146F VAL* 4.5 9.2 - - + -
165F ALA 5.0 0.2 - - - +
168F ALA* 3.8 27.1 - - + +
169F LEU* 3.7 36.6 - - + +
172F ALA* 4.0 18.8 - - + -
174F VAL* 5.5 2.0 - - + -
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Residues in contact with SER 67 (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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87C PRO* 4.3 14.0 + - - +
90C SER 5.1 0.9 + - - -
91C SER* 4.0 17.4 + - - -
49F ALA* 6.1 0.9 - - - +
50F LYS* 5.1 1.8 - - - +
65F ALA 4.2 0.6 - - - -
66F VAL* 1.3 85.3 - - - +
68F GLY* 1.3 68.1 + - - +
70F ARG* 4.3 14.9 + - - -
144F LEU* 4.0 2.8 - - - +
145F GLU* 3.2 45.9 + - - +
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Residues in contact with GLY 68 (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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91C SER* 5.4 1.4 + - - -
50F LYS* 3.7 22.7 - - - +
66F VAL* 3.7 3.3 + - - -
67F SER* 1.3 80.4 - - - +
69F PRO* 1.3 77.9 - - - +
70F ARG* 3.5 10.6 + - - +
143F GLN 3.8 5.4 - - - +
144F LEU* 4.0 3.4 - - - -
145F GLU* 5.2 0.9 + - - +
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Residues in contact with PRO 69 (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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50F LYS* 3.4 23.6 - - + +
68F GLY* 1.3 83.7 - - - +
70F ARG* 1.3 59.5 + - - +
71F GLN* 5.2 4.4 + - - -
139F TYR* 4.0 25.4 - - + -
142F ALA* 4.4 15.9 - - + -
143F GLN 3.6 9.4 - - - +
144F LEU* 3.8 16.4 - - + -
174F VAL* 5.1 4.5 - - + -
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Residues in contact with ARG 70 (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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91C SER* 4.1 34.4 + - - +
67F SER* 4.3 10.5 + - - -
68F GLY 3.5 7.4 + - - +
69F PRO* 1.3 75.2 - - - +
71F GLN* 1.3 74.2 + - - +
142F ALA* 3.4 24.0 - - - -
143F GLN* 3.6 39.4 + - + +
145F GLU* 4.1 27.1 + - - +
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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