Contacts of the strand formed by residues 61 - 68 (chain G) in PDB entry 1A81
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 ALA 61 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26G GLU* 4.1 30.8 - - + +
29G LEU* 4.6 11.7 - - + -
34G MET* 4.1 12.8 - - + +
55G VAL 3.5 5.2 - - - +
60G LYS* 1.3 77.6 - - - +
62G HIS* 1.3 72.0 + - - +
63G HIS* 4.2 13.7 - - + +
184K ILE* 5.3 3.8 - - + +
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Residues in contact with HIS 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G LEU 3.1 4.0 - - - +
54G SER* 3.5 0.5 - - - -
55G VAL* 2.8 56.8 + - + +
57G HIS* 2.8 44.7 + + + +
60G LYS* 3.6 15.1 + - + -
61G ALA* 1.3 83.1 + - - +
63G HIS* 1.3 63.9 + - - +
64G TYR* 3.9 16.8 + - + -
100G VAL* 4.1 25.6 - - + +
182H SER* 3.3 17.6 + - - +
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Residues in contact with HIS 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G ARG* 3.7 33.3 - - + +
25G ALA* 4.7 1.6 - - + -
26G GLU* 3.1 42.2 + - + +
29G LEU* 6.1 0.2 - - + -
42G ARG* 2.4 34.7 + - - +
52G ALA* 5.5 0.4 - - + -
53G LEU 3.1 3.4 - - - +
54G SER* 2.6 22.2 + - - -
61G ALA* 4.2 12.0 - - + +
62G HIS* 1.3 77.6 - - - +
64G TYR* 1.3 63.4 + - - +
180H LEU 5.3 0.2 - - - -
181H PTR 3.8 21.7 - - + -
182H SER* 2.8 36.9 + - - +
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Residues in contact with TYR 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G ALA* 3.0 4.3 - - - +
53G LEU* 2.4 57.7 + - + +
55G VAL* 4.4 11.7 - - + -
62G HIS* 3.9 22.2 - - + -
63G HIS* 1.3 78.9 - - - +
65G THR* 1.3 62.0 + - - +
66G ILE* 3.9 0.5 + - - +
76G ILE* 4.4 20.9 - - + -
98G GLY 4.1 1.6 + - - -
99G LEU* 3.3 34.8 - - + +
100G VAL* 3.5 26.7 + - - +
181H PTR 4.8 0.4 - - - -
182H SER* 3.6 29.9 - - - -
183H GLY 3.5 31.9 + - - -
184H LEU* 3.8 8.1 - - + -
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Residues in contact with THR 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G SER* 4.8 7.2 + - - -
46G ASN* 5.7 3.9 + - - +
47G TYR* 4.0 32.0 - - + +
51G PHE 3.4 10.0 + - - -
52G ALA* 4.1 2.0 - - - +
64G TYR* 1.3 75.5 - - - +
66G ILE* 1.3 64.0 + - - +
67G GLU* 3.6 8.0 + - - +
76G ILE* 3.5 24.1 - - + +
77G ALA 4.3 0.5 + - - -
181H PTR 3.7 34.3 - - + -
182H SER 5.1 2.6 + - - +
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Residues in contact with ILE 66 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G LEU* 4.2 16.2 - - + -
50G GLY* 3.5 4.0 - - - -
51G PHE* 2.7 44.6 + - + +
52G ALA 4.4 0.7 - - - -
53G LEU* 4.1 35.9 - - + +
64G TYR 4.7 0.4 - - - +
65G THR* 1.3 73.1 - - - +
67G GLU* 1.3 59.1 + - - +
74G TYR* 3.7 29.6 - - + -
75G ALA* 4.2 5.8 - - - +
76G ILE* 3.3 30.7 - - + -
85G PRO* 5.3 8.1 - - + -
88G LEU* 4.6 13.7 - - + -
89G CYS* 6.3 1.3 - - - -
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Residues in contact with GLU 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G TYR* 3.4 43.4 + - + -
50G GLY* 4.9 2.0 - - - -
65G THR* 4.2 8.8 + - - +
66G ILE* 1.3 72.5 - - - +
68G ARG* 1.3 63.6 + - - +
69G GLU* 3.5 10.5 + - - +
74G TYR* 3.5 1.7 - - - -
75G ALA 3.0 38.6 + - - +
77G ALA* 3.7 28.4 - - + +
225G LYS* 5.0 7.4 - - - -
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Residues in contact with ARG 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G TYR* 6.2 0.2 - - - +
48G LEU 4.6 7.9 + - - +
49G GLY* 3.9 28.2 + - - +
50G GLY* 4.6 3.0 - - - -
66G ILE 3.8 1.2 + - - -
67G GLU* 1.3 72.9 - - - +
69G GLU* 1.3 79.0 + - - +
70G LEU* 3.6 6.8 + - - +
72G GLY* 3.2 28.9 + - - -
73G THR 3.6 3.1 - - - -
74G TYR* 3.7 32.4 + - + -
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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