Contacts of the strand formed by residues 63 - 70 (chain B) in PDB entry 1AGQ
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 GLU 63 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B HIS* 2.8 35.6 + - + +
49B LEU 3.3 6.7 - - - +
50B ASN* 3.2 26.1 + - - +
51B VAL* 4.5 0.4 - - - -
61B LYS 3.4 13.6 + - - +
62B GLU* 1.3 85.2 - - - +
64B LEU* 1.3 68.0 + - - +
112B LEU* 4.9 1.7 - - - +
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Residues in contact with LEU 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 HIS* 3.4 5.5 - - - -
49B LEU* 2.8 54.1 + - + +
50B ASN 4.2 0.4 - - - -
51B VAL* 3.8 25.4 - - + +
54B LEU* 4.3 17.0 - - + -
63B GLU* 1.3 80.5 - - - +
65B ILE* 1.3 75.3 + - - +
66B PHE* 3.6 14.8 + - + +
112B LEU* 4.4 15.0 - - + -
127B HIS* 3.9 30.7 - - + +
128B SER* 5.3 0.4 - - - -
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Residues in contact with ILE 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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46B ALA* 3.7 28.9 - - + -
47B ILE 3.6 5.6 - - - +
48B HIS* 3.9 31.4 - - + +
64B LEU* 1.3 77.6 - - - +
66B PHE* 1.3 61.3 + - - +
67B ARG* 3.8 11.7 + - + +
109B ASP* 4.3 4.7 - - - +
128B SER* 3.6 9.0 + - - -
47D ILE* 6.4 0.2 - - + -
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Residues in contact with PHE 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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80A TYR* 3.9 27.8 - + - -
83A ILE* 4.2 24.2 - - + -
84A LEU* 4.0 14.8 - - + -
87A LEU* 3.8 21.8 - - + -
45B THR 3.8 0.2 - - - +
46B ALA* 3.4 1.7 - - - -
47B ILE* 2.8 51.2 + - + +
49B LEU* 3.7 21.3 - - + -
54B LEU* 5.0 0.9 - - + -
64B LEU* 3.6 16.3 + - + -
65B ILE* 1.3 73.4 - - - +
67B ARG* 1.3 63.0 + - - +
68B TYR* 3.8 22.4 - + + -
127B HIS 3.1 28.0 - - - -
128B SER* 3.6 5.4 - - - -
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Residues in contact with ARG 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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80A TYR* 3.5 7.8 - - - -
44B LEU* 3.8 31.3 - - + +
45B THR 3.1 5.6 - - - +
46B ALA* 3.8 23.1 - - + -
65B ILE* 4.1 11.7 - - + +
66B PHE* 1.3 83.6 - - - +
68B TYR* 1.3 62.6 + - - +
109B ASP* 2.8 28.2 + - - -
128B SER* 2.8 10.6 + - - +
129B ALA* 2.9 41.1 + - - +
130B LYS* 3.7 19.2 + - - +
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Residues in contact with TYR 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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80A TYR* 3.3 14.4 - - + +
84A LEU* 3.9 16.6 - - + -
87A LEU* 6.4 0.9 - - + -
98A VAL 4.8 11.9 - - - -
43B VAL 3.7 0.7 - - - +
44B LEU* 3.5 2.6 - - - -
45B THR* 2.8 64.6 + - + +
47B ILE* 4.6 7.9 - - + -
66B PHE* 3.8 27.4 - + + -
67B ARG* 1.3 75.0 - - - +
69B CYS* 1.3 73.9 + - - +
70B SER* 3.9 19.1 - - - -
129B ALA* 4.3 0.9 - - - -
48D HIS* 2.6 34.1 + + - -
65D ILE* 4.1 7.3 - - - +
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Residues in contact with CYS 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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80A TYR* 3.0 10.4 + - - +
99A GLY* 3.2 21.7 - - - -
43B VAL 3.4 0.9 - - - -
68B TYR* 1.3 74.9 - - - +
70B SER* 1.3 65.4 + - - +
103B CYS* 3.8 6.3 - - - +
104B ARG* 3.8 18.4 - - - -
105B PRO* 3.6 20.9 - - - -
129B ALA* 3.6 13.0 - - - -
132B CYS* 2.0 58.3 - - + -
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Residues in contact with SER 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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98A VAL* 4.4 11.2 - - - -
99A GLY* 4.2 15.7 - - - +
41B GLY 3.3 1.4 - - - +
43B VAL* 2.9 34.7 + - - +
45B THR* 4.4 5.7 + - - -
68B TYR* 3.9 20.4 - - - -
69B CYS* 1.3 77.3 - - - +
71B GLY* 1.3 59.0 + - - +
103B CYS* 3.4 11.7 - - - -
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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