Contacts of the strand formed by residues 71 - 76 (chain B) in PDB entry 5A0Q
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 ILE 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B PRO* 3.6 4.3 - - - +
67B ILE* 3.2 29.3 + - + -
68B THR* 3.0 32.1 + - + +
70B HIS* 1.3 83.4 - - - +
72B GLY* 1.3 82.8 + - - +
104B ILE 4.3 7.4 - - - +
106B THR* 3.4 43.5 - - + +
109B LEU* 4.1 22.4 - - + -
135B ILE* 3.5 18.2 - - + -
136B CYS 3.7 7.4 - - - +
137B GLY* 4.4 1.1 - - - -
139B ASN* 6.0 0.9 - - - +
217B PHE* 3.9 9.2 - - - -
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Residues in contact with GLY 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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45B LEU* 4.7 3.6 - - - -
65B GLU 3.7 11.7 - - - -
66B PRO* 4.2 1.3 - - - -
67B ILE* 4.1 2.0 - - - -
71B ILE* 1.3 84.0 - - - +
73B LEU* 1.3 62.3 + - - -
135B ILE* 3.4 5.4 - - - +
136B CYS 3.3 26.3 + - - -
217B PHE* 3.8 19.7 - - - -
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Residues in contact with LEU 73 (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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45B LEU* 4.0 2.5 - - - -
63B LYS 3.1 10.8 - - - +
64B VAL* 3.3 11.6 - - - +
65B GLU 3.5 5.7 + - - +
67B ILE* 3.4 32.3 - - + -
72B GLY* 1.3 71.2 - - - -
74B VAL* 1.3 68.2 + - - +
82B TYR* 3.4 20.4 - - + +
85B LEU* 4.5 3.8 - - + -
86B VAL* 3.7 27.8 - - + -
89B ALA* 4.6 7.2 - - + -
113B VAL* 6.2 0.2 - - + -
133B LEU* 2.8 42.0 - - + -
134B LEU 3.3 4.5 - - - -
135B ILE* 3.4 24.9 - - + -
217B PHE* 5.3 0.2 - - - -
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Residues in contact with VAL 74 (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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34B SER* 3.4 31.4 - - - +
35B VAL 5.3 0.2 - - - +
45B LEU* 3.5 36.1 - - + +
46B ALA 4.3 4.0 - - - +
47B THR* 4.1 17.3 - - + -
63B LYS* 3.4 6.5 - - + +
64B VAL* 3.9 25.4 - - + -
73B LEU* 1.3 80.7 - - - +
75B TYR* 1.4 63.8 + - - +
133B LEU* 3.1 4.4 - - - -
134B LEU* 2.9 33.4 + - + -
162B MET* 3.5 2.6 - - - +
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Residues in contact with TYR 75 (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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159A TYR* 5.6 3.1 - - - -
32B ALA 4.7 0.2 - - - +
34B SER* 3.2 14.4 + - - -
47B THR* 4.6 0.2 + - - -
61B VAL* 5.2 8.0 + - + +
62B HIS 5.0 0.4 - - - -
63B LYS* 3.4 65.3 + - + +
74B VAL* 1.4 74.5 - - - +
76B SER* 1.3 70.0 - - - +
77B GLY 3.7 10.1 - - - -
78B MET 3.9 11.4 - - - -
79B GLY* 3.5 31.7 - - - -
82B TYR* 3.2 53.2 - + + -
83B ARG* 4.9 4.0 + - - -
131B VAL* 3.9 9.6 - - + -
132B SER 3.5 10.3 - - - +
133B LEU* 3.9 1.3 - - + -
162B MET* 4.2 0.4 - - - -
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Residues in contact with SER 76 (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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28B VAL* 3.6 15.8 - - - +
30B GLY 4.5 0.7 - - - -
31B GLY* 5.1 0.9 - - - -
32B ALA 3.9 11.0 - - - -
34B SER* 4.0 5.2 - - - -
63B LYS* 5.5 0.7 - - - +
75B TYR* 1.3 78.6 - - - +
77B GLY* 1.3 60.0 + - - +
131B VAL* 3.6 2.3 - - - -
132B SER* 2.9 33.8 + - - +
162B MET* 3.4 12.0 - - - +
163B GLY* 3.4 38.8 + - - -
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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