Contacts of the strand formed by residues 68 - 75 (chain B) in PDB entry 3AG9
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 HIS 68 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B ILE* 4.6 11.7 - - + -
59B LEU* 4.2 22.1 - - + +
60B VAL 3.3 13.1 + - - +
61B LYS* 3.3 31.1 - - + +
66B GLY 3.6 13.2 - - - -
67B ASN* 1.3 72.9 - - - +
69B TYR* 1.3 76.5 + - - +
121B GLU* 4.8 1.2 - - - +
122B TYR* 4.2 19.2 + + + +
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Residues in contact with TYR 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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77A GLN* 3.4 25.1 + - - -
342A LYS* 5.7 0.5 + - - +
43B PHE* 4.3 5.2 - + - -
58B MET 3.5 0.7 - - - +
59B LEU* 3.5 6.2 - - - +
60B VAL* 2.9 38.0 + - + +
62B HIS* 3.7 22.9 - - + -
65B THR* 4.2 1.6 + - - -
67B ASN* 3.3 33.5 + - + +
68B HIS* 1.3 86.3 - - - +
70B ALA* 1.3 60.0 + - - +
71B MET 3.8 0.2 - - - -
107B GLU* 3.5 31.5 + - + +
108B PHE* 3.8 17.1 - + - -
119B VAL* 3.5 27.4 - - + -
120B MET 3.3 18.2 - - - +
121B GLU* 4.2 7.4 - - + -
122B TYR* 3.7 10.9 - - - +
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Residues in contact with ALA 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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49B LEU* 4.1 8.5 - - + -
57B VAL* 3.9 12.1 - - + -
58B MET 3.5 5.8 - - - -
69B TYR* 1.3 72.1 - - - +
71B MET* 1.3 59.2 + - - +
72B LYS 4.0 0.4 - - - -
120B MET* 2.7 42.8 + - + +
122B TYR* 3.8 5.2 - - - +
351B A02 3.4 46.4 - - + +
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Residues in contact with MET 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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40B LEU* 4.1 23.8 - - + -
43B PHE* 5.0 6.1 - - + -
45B ARG* 4.7 5.6 - - + +
56B ARG 3.6 0.9 - - - +
57B VAL* 3.2 3.4 - - - -
58B MET* 2.6 48.5 + - + +
60B VAL* 3.7 35.7 - - + -
69B TYR 3.8 0.8 + - - -
70B ALA* 1.3 70.4 - - - +
72B LYS* 1.3 63.3 + - - +
73B ILE* 3.3 36.8 + - + +
110B PHE* 4.6 4.9 - - - -
117B TYR* 3.8 20.4 - - + -
118B MET 3.6 2.9 - - - -
119B VAL* 3.9 23.6 - - + +
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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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56B ARG 3.3 9.4 - - - +
57B VAL* 4.0 21.5 - - + +
70B ALA 3.8 1.4 + - - -
71B MET* 1.3 70.5 - - - +
73B ILE* 1.3 62.1 + - - +
74B LEU* 3.7 28.4 - - + +
91B GLU* 2.7 40.8 + - - -
116B LEU 3.6 1.0 - - - +
117B TYR* 3.3 5.4 - - - +
118B MET* 2.8 54.1 + - + +
120B MET* 5.3 7.9 - - + -
183B THR* 5.9 0.2 + - - -
184B ASP* 4.0 19.8 + - - +
351B A02 4.3 15.5 - - + +
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Residues in contact with ILE 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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55B GLY* 3.0 5.0 - - - -
56B ARG* 2.7 39.0 + - + +
58B MET* 3.7 19.5 - - + -
71B MET* 3.3 27.4 - - + +
72B LYS* 1.3 74.5 - - - +
74B LEU* 1.3 63.7 + - - +
75B ASP 4.1 0.2 + - - -
115B ASN* 3.8 23.8 - - + +
116B LEU 3.4 3.1 - - - -
117B TYR* 3.7 34.1 - - + -
335B ILE* 3.3 35.9 - - + -
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Residues in contact with LEU 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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54B PHE* 3.6 15.9 - - + -
55B GLY* 4.0 1.6 - - - -
72B LYS* 3.7 36.6 - - + +
73B ILE* 1.3 76.7 - - - +
75B ASP* 1.3 61.5 + - - +
76B LYS 3.3 0.7 + - - -
79B VAL* 4.0 12.3 - - + -
88B THR* 3.5 36.6 - - + +
91B GLU* 4.9 4.9 - - - +
115B ASN* 3.1 7.9 - - - -
116B LEU* 2.8 50.9 + - + +
118B MET* 5.0 8.5 - - + -
351B A02 3.9 24.5 - - + -
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Residues in contact with ASP 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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54B PHE 2.9 15.3 + - - +
55B GLY* 4.6 0.8 - - - -
73B ILE* 4.1 2.0 + - - +
74B LEU* 1.3 68.1 - - - +
76B LYS* 1.3 64.9 + - - +
77B GLN* 3.1 26.5 + - - +
78B LYS* 3.1 39.0 + - + +
79B VAL* 2.9 23.3 + - - +
114B SER* 4.4 4.4 - - - +
115B ASN* 3.5 13.9 + - - +
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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