Contacts of the strand formed by residues 64 - 70 (chain A) in PDB entry 6P59
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 LEU 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A PHE* 3.9 16.4 - - + -
19A ARG 4.7 0.4 - - - +
20A LYS* 4.4 4.7 - - + +
21A LEU* 3.6 45.3 - - + +
58A VAL* 3.3 4.3 - - - +
59A ALA* 3.2 27.5 + - + -
62A THR* 3.0 13.8 + - - +
63A ASN* 1.3 81.9 + - - +
65A SER* 1.3 69.8 + - - +
66A LEU* 5.9 4.3 - - + -
10B PRO* 4.7 9.4 - - + -
11B VAL 4.1 4.9 - - - +
12B TRP* 3.6 49.1 - - + +
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Residues in contact with SER 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ALA* 4.6 1.0 - - - +
57A PHE 3.2 14.6 - - - -
58A VAL* 3.5 18.4 - - - -
59A ALA 4.9 0.2 - - - +
64A LEU* 1.3 80.0 - - - +
66A LEU* 1.3 66.2 + - - +
67A GLN* 4.3 2.3 + - - +
10B PRO* 3.8 2.6 - - - +
11B VAL* 2.6 62.1 + - - +
13B ARG* 3.9 21.8 + - - +
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 5.6 7.4 - - + -
27A ILE* 6.2 0.7 - - + -
56A ALA* 3.3 4.3 - - - -
57A PHE* 2.8 37.5 + - + +
64A LEU* 5.9 4.5 - - + -
65A SER* 1.3 75.4 - - - +
67A GLN* 1.3 60.9 + - - +
68A PHE* 3.6 21.0 - - + -
99A ALA* 4.5 6.5 - - + -
101A MET* 3.5 33.0 - - + -
110A TRP* 3.5 53.2 - - + +
8B VAL* 4.6 4.9 - - + -
9B ARG 4.2 0.2 - - - -
10B PRO* 4.4 11.4 - - + -
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Residues in contact with GLN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLU* 3.6 17.3 - - - +
55A ILE 3.2 18.0 + - - -
56A ALA* 3.7 14.3 - - - +
65A SER* 3.5 2.6 + - - +
66A LEU* 1.3 70.9 - - - +
68A PHE* 1.3 82.2 + - - +
69A PHE* 3.3 38.2 + - + -
7B ILE 3.7 0.9 - - - +
8B VAL* 3.3 2.8 - - - -
9B ARG* 3.1 39.8 + - + +
11B VAL* 3.7 21.5 - - + +
13B ARG* 4.1 3.3 + - - -
76B LEU* 3.2 26.7 - - + +
77B THR* 5.6 0.2 + - - -
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Residues in contact with PHE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLU* 3.6 3.6 - - - -
55A ILE* 2.9 40.4 + - + +
57A PHE* 4.0 22.2 - + - -
66A LEU* 3.6 28.9 - - + -
67A GLN* 1.3 87.1 + - - +
69A PHE* 1.3 60.6 + - - +
85A TYR* 3.7 25.1 - - + -
86A VAL* 3.6 18.6 - - + -
97A LEU* 4.2 18.2 - - + -
98A LYS 3.7 11.9 - - - -
99A ALA* 4.2 10.1 - - + -
110A TRP* 5.5 0.4 - + - -
6B TRP* 3.7 11.2 - + + -
7B ILE 3.3 5.6 - - - -
8B VAL* 3.7 28.0 - - + -
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Residues in contact with PHE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLU* 4.1 4.5 - - + -
67A GLN* 3.3 40.6 - - + -
68A PHE* 1.3 79.3 - - - +
70A PRO* 1.3 65.9 - - + +
71A ALA 3.2 0.3 + - - -
74A GLN* 3.6 27.6 - - + -
6B TRP* 3.2 9.9 - - - -
7B ILE* 2.7 47.7 + - + +
9B ARG* 5.6 7.0 - - + -
11B VAL* 5.2 0.9 - - + -
53B TRP* 3.7 37.7 - + + -
73B TYR* 3.8 45.8 - + - -
76B LEU* 3.9 9.9 - - + -
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Residues in contact with PRO 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLY 3.5 23.8 - - - +
52A ARG 4.1 4.5 - - - -
53A SER 3.3 23.3 - - - +
54A GLU* 4.2 1.1 - - - -
69A PHE* 1.3 81.9 - - + +
71A ALA* 1.3 64.7 + - - +
72A SER* 3.2 2.5 - - - +
73A TRP* 3.0 21.7 + - + +
74A GLN* 3.4 10.9 + - - +
4B LYS* 3.5 15.7 - - + +
5B MET 3.6 7.4 - - - +
6B TRP* 4.1 1.0 - - + -
53B TRP* 3.6 32.3 - - + -
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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