Contacts of the strand formed by residues 61 - 70 (chain B) in PDB entry 5XFR
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 PHE 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B LEU* 3.8 30.4 - - + +
54B ALA 3.4 4.7 - - - -
55B ARG* 3.4 63.5 - - + -
59B GLY 4.9 3.1 - - - -
60B LEU* 1.3 75.5 - - - +
62B TYR* 1.3 59.4 + - - +
92B ASP* 3.9 10.3 - - - -
94B GLN* 3.7 25.4 - - + -
153B GLN* 3.6 24.5 - - + -
156B PHE* 6.1 5.2 - - + -
157B ALA* 5.7 12.3 - - + -
38D PRO* 3.3 30.1 - - - +
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Residues in contact with TYR 62 (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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53B LEU* 3.6 5.3 - - - -
54B ALA* 2.7 41.8 + - - +
56B TRP* 3.6 19.7 - - + -
58B ASP* 2.8 23.7 + - - -
60B LEU* 3.4 26.8 - - + +
61B PHE* 1.3 73.1 - - - +
63B LEU* 1.3 64.1 + - - +
64B GLY 3.5 0.2 + - - -
80B PHE* 3.8 20.0 - - + -
162B ARG* 2.9 23.1 + - - -
36D M3L 3.6 62.3 - - + -
37D LYS 3.9 11.2 - - - -
38D PRO* 3.8 19.2 - - + +
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Residues in contact with LEU 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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51B ASP* 4.7 17.0 - - + +
52B VAL 3.6 11.2 - - - +
53B LEU* 3.7 15.1 - - + +
62B TYR* 1.3 73.8 - - - +
64B GLY* 1.3 68.7 + - - +
65B THR* 5.5 1.6 - - - +
80B PHE* 3.8 10.6 - - - -
81B GLU* 3.8 48.5 + - + +
36D M3L 6.0 0.5 - - - +
37D LYS 5.2 3.6 + - - +
38D PRO 6.1 0.4 - - - -
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Residues in contact with GLY 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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51B ASP* 3.5 5.9 - - - +
52B VAL* 2.9 35.3 + - - -
54B ALA* 5.9 0.2 - - - -
62B TYR 3.5 2.3 + - - -
63B LEU* 1.3 83.0 - - - +
65B THR* 1.3 63.8 + - - -
78B ILE* 3.8 13.9 - - - -
79B ILE 3.3 12.3 - - - -
80B PHE* 4.4 2.0 - - - -
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Residues in contact with THR 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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49B GLY* 3.8 29.2 - - - +
50B GLN 3.5 3.1 - - - +
51B ASP* 3.2 16.2 + - - +
63B LEU* 5.5 1.9 - - - +
64B GLY* 1.3 74.1 - - - -
66B ILE* 1.3 69.9 + - - +
67B LYS* 3.2 3.1 + - - -
78B ILE* 3.6 5.3 - - - +
79B ILE* 3.0 45.7 + - + +
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Residues in contact with ILE 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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46B PHE* 3.7 32.8 - - + -
47B GLU 3.8 14.1 - - - +
48B GLU* 3.4 2.2 - - - -
49B GLY* 2.5 34.8 + - - -
50B GLN* 3.0 20.3 + - + +
52B VAL* 3.8 33.4 - - + -
64B GLY 4.3 0.2 - - - -
65B THR* 1.3 70.0 - - - +
67B LYS* 1.3 56.6 + - - +
68B LYS 3.4 23.6 - - - +
69B ILE* 3.8 16.2 - - + -
76B CYS* 4.1 16.8 - - + -
77B PHE 4.0 3.8 - - - -
78B ILE* 4.6 4.0 - - + -
93B ILE* 5.0 1.3 - - + -
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Residues in contact with LYS 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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48B GLU* 2.9 26.5 - - - +
49B GLY 4.8 0.2 - - - +
65B THR* 3.2 5.9 + - + +
66B ILE* 1.3 74.8 - - - +
68B LYS* 1.3 84.4 + - + +
77B PHE* 2.9 24.2 + - + +
79B ILE* 4.9 13.2 - - + +
85B LYS* 3.6 29.9 - - - +
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Residues in contact with LYS 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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48B GLU* 4.3 6.1 - - - +
66B ILE* 3.4 8.3 - - - +
67B LYS* 1.3 101.1 - - + +
69B ILE* 1.3 69.9 + - - +
76B CYS* 3.5 1.7 - - - -
77B PHE* 3.2 58.9 + - + -
87B TRP* 4.2 15.7 - - + -
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Residues in contact with ILE 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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46B PHE* 3.8 18.4 - - + +
47B GLU* 3.7 36.1 - - - +
48B GLU* 4.2 13.1 - - + +
66B ILE* 3.8 10.3 - - + -
68B LYS* 1.3 83.2 - - - +
70B ASN* 1.3 71.3 + - - +
71B ILE* 3.8 11.1 + - + +
75B SER 4.0 4.5 - - - +
76B CYS* 4.1 7.6 - - - -
87B TRP* 4.6 2.9 - - - -
90B TRP* 4.4 15.0 - - + +
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Residues in contact with ASN 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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69B ILE* 1.3 73.0 + - - +
71B ILE* 1.3 67.9 + - - +
72B LEU* 3.3 3.2 + - - +
73B LYS* 3.2 44.6 + - + +
74B GLN 3.5 5.7 + - - -
75B SER 3.0 18.4 + - - +
87B TRP* 3.7 30.2 - - + -
90B TRP* 3.5 10.9 - - - -
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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