Contacts of the strand formed by residues 59 - 72 (chain B) in PDB entry 6IY6
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 VAL 59 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B GLU* 1.3 70.7 - - - +
60B VAL* 1.3 62.2 + - - +
61B TRP* 5.8 1.6 - - + -
117B GLU* 4.0 22.4 - - + +
118B GLY 3.6 6.1 - - - +
119B VAL* 4.2 15.7 - - + -
140B GLN* 3.9 19.7 - - - +
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Residues in contact with VAL 60 (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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44B VAL 5.5 0.2 - - - -
46B VAL* 4.0 25.8 - - + -
51B LEU* 3.8 24.9 - - + -
55B LYS* 4.6 10.3 - - + +
58B GLU* 4.1 24.2 - - + +
59B VAL* 1.3 76.8 - - - +
61B TRP* 1.3 63.4 + - - +
62B VAL* 4.4 4.2 - - + +
116B VAL 3.8 0.7 - - - +
117B GLU* 3.6 3.1 - - - +
118B GLY 3.0 33.8 + - - +
120B VAL* 3.9 16.6 - - + -
137B LEU* 4.1 9.2 - - + -
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Residues in contact with TRP 61 (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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43B ARG* 3.5 56.6 - - + +
44B VAL 3.6 18.3 + - - +
45B LEU* 3.7 13.9 - - + -
46B VAL* 2.9 28.9 + - - +
59B VAL* 5.8 2.2 - - + -
60B VAL* 1.3 73.9 - - - +
62B VAL* 1.3 63.6 + - - +
115B ASP* 4.0 22.0 - - + -
116B VAL 3.2 11.0 - - - -
117B GLU* 3.5 62.1 + - + -
141B LYS* 4.2 19.7 - - + -
143B TYR* 4.4 12.8 - + - -
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 4.6 3.1 - - - +
46B VAL* 3.8 27.1 - - + +
48B VAL* 4.1 18.4 - - + -
51B LEU* 3.9 19.5 - - + -
60B VAL* 4.4 9.4 - - + -
61B TRP* 1.3 78.8 - - - +
63B ARG* 1.3 62.4 + - - +
64B ALA* 4.0 21.3 + - + -
80B LEU* 4.8 8.7 - - + -
82B GLN* 5.3 0.4 - - - +
114B VAL 3.5 2.4 - - - +
115B ASP* 3.5 0.8 - - - -
116B VAL* 2.7 46.2 + - + +
137B LEU* 4.4 13.0 - - + -
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Residues in contact with ARG 63 (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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295A PHE 3.5 5.7 + - - -
296A ASN* 2.5 37.1 + - - +
297A TYR* 3.1 30.1 - - - -
464A PRO* 6.1 2.0 - - - -
465A PRO* 3.4 23.5 - - - +
35B ILE* 3.5 14.5 - - - +
45B LEU* 3.8 29.4 - - + +
46B VAL 4.9 1.7 + - - +
62B VAL* 1.3 72.7 - - - +
64B ALA* 1.3 60.8 + - - +
82B GLN* 4.2 20.6 + - - +
113B ILE* 3.7 24.0 - - + -
114B VAL 3.3 4.3 - - - +
115B ASP* 2.7 28.1 + - - +
145B ILE* 4.3 4.2 - - - +
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Residues in contact with ALA 64 (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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48B VAL* 4.4 5.4 - - + -
62B VAL* 3.9 13.4 - - + -
63B ARG* 1.3 72.8 - - - +
65B ARG* 1.3 59.7 + - - +
80B LEU* 3.8 29.4 - - + -
81B ARG 3.3 17.7 - - - +
82B GLN* 4.6 2.0 - - + -
113B ILE* 3.4 5.9 - - - +
114B VAL* 2.8 38.3 + - - +
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Residues in contact with ARG 65 (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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258A ILE 4.6 0.8 + - - -
259A CYS 3.1 19.2 + - - -
261A ASP* 2.6 34.3 + - - +
462A GLY* 2.4 30.4 + - - -
464A PRO* 4.2 5.1 - - - +
64B ALA* 1.3 72.8 - - - +
66B VAL* 1.3 62.0 - - - +
67B HIS 3.5 1.1 + - - -
80B LEU* 3.3 7.7 - - - -
81B ARG* 2.9 65.8 + - - +
82B GLN* 6.1 0.9 - - - +
111B GLU* 3.0 30.1 + - - +
112B SER 3.4 5.6 - - - -
113B ILE* 3.9 20.7 - - + +
188B ARG* 3.0 25.8 - - - +
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Residues in contact with VAL 66 (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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65B ARG* 1.3 71.1 - - - +
67B HIS* 1.3 61.6 + - - +
68B THR* 4.3 7.9 - - - +
69B SER* 3.8 29.8 - - - +
78B LEU* 4.0 22.0 - - + -
79B VAL 3.9 2.7 - - - +
80B LEU* 4.6 3.4 - - + -
108B ILE* 3.7 29.8 - - + +
109B ASN 4.5 4.7 - - - +
110B LYS* 3.9 4.3 - - + -
111B GLU* 2.9 25.9 + - - +
112B SER 3.1 17.9 + - - +
114B VAL* 4.0 19.7 - - + -
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Residues in contact with HIS 67 (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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65B ARG 3.5 2.0 + - - -
66B VAL* 1.3 74.1 - - - +
68B THR* 1.3 66.0 + - + +
79B VAL* 2.8 40.8 + - + +
81B ARG* 3.3 44.7 + - + -
86B ASN* 4.5 10.6 + - - -
110B LYS* 4.5 7.6 - - - +
111B GLU* 4.2 9.6 - - - +
602B PO4 3.7 19.3 + - - -
604B PO4 3.6 21.7 + - - -
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Residues in contact with THR 68 (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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66B VAL* 4.3 5.0 - - - +
67B HIS* 1.3 83.4 - - + +
69B SER* 1.3 62.2 + - - +
70B ARG* 4.1 5.8 + - + +
77B PHE 4.3 0.2 - - - +
78B LEU* 3.5 1.6 - - - -
79B VAL* 2.8 51.2 + - + +
110B LYS* 5.5 3.4 - - - -
604B PO4 3.3 32.5 + - - +
179H ARG* 4.5 7.1 + - - -
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Residues in contact with SER 69 (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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66B VAL* 3.8 17.9 - - - +
68B THR* 1.3 76.9 + - - +
70B ARG* 1.3 59.4 + - - +
71B ALA* 4.0 1.7 + - - +
76B CYS* 4.8 1.1 - - - -
77B PHE 3.4 10.3 - - - -
78B LEU* 4.2 12.8 - - - +
105B ALA 4.4 7.2 - - - -
106B ALA* 3.8 23.7 + - - +
108B ILE 4.1 8.8 + - - -
110B LYS* 5.9 3.8 - - - +
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Residues in contact with ARG 70 (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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68B THR* 4.1 6.6 + - + +
69B SER* 1.3 72.2 - - - +
71B ALA* 1.3 62.3 + - - +
72B LYS* 6.1 2.1 - - + +
76B CYS* 4.1 0.2 - - - -
77B PHE* 2.8 49.4 + - + +
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Residues in contact with ALA 71 (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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69B SER 4.0 1.7 + - - +
70B ARG* 1.3 79.9 - - - +
72B LYS* 1.3 59.4 + - - +
73B GLY 4.3 0.4 - - - -
75B GLN 3.7 12.6 - - - +
76B CYS* 3.9 8.5 - - + +
77B PHE* 6.1 0.7 - - - -
102B VAL* 5.5 1.8 - - + +
106B ALA* 3.7 30.1 - - + -
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Residues in contact with LYS 72 (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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70B ARG* 6.1 3.1 - - + +
71B ALA* 1.3 73.2 - - - +
73B GLY* 1.3 63.6 + - - +
74B LYS 3.1 4.3 + - - -
75B GLN* 3.0 21.7 + - + +
77B PHE* 6.3 0.6 - - - -
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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