Contacts of the strand formed by residues 73 - 78 (chain H) in PDB entry 6CP3
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 GLY 73 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212G TYR* 4.4 4.7 - - - -
51H GLN* 3.7 0.2 - - - -
52H LEU* 2.9 35.5 + - - +
72H GLY* 1.3 75.9 - - - -
74H PHE* 1.3 70.9 + - - -
86H THR 3.3 10.5 - - - -
87H ALA* 4.3 2.2 - - - -
10I TYR* 3.1 9.2 + - - -
14I LEU* 3.5 14.2 - - - +
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Residues in contact with PHE 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G GLU* 6.1 1.8 - - + -
205G VAL* 4.1 7.6 - - + -
208G ASP* 4.2 3.1 - - + -
209G LEU* 3.6 45.3 - - + -
212G TYR* 3.5 45.3 - + + -
49H VAL* 3.9 17.3 - - + -
50H GLU 3.6 6.3 - - - -
51H GLN* 3.6 34.3 - - + -
52H LEU* 3.5 6.7 - - - +
73H GLY* 1.3 83.8 - - - -
75H ALA* 1.3 59.5 + - - +
76H THR* 4.1 9.8 + - - +
84H CYS 3.9 0.7 - - - +
85H VAL* 3.5 2.3 - - - -
86H THR* 2.9 42.3 + - - +
10I TYR* 3.6 15.5 - + - -
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Residues in contact with ALA 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H LEU* 3.9 24.0 - - + -
48H THR 3.8 1.9 - - - +
49H VAL* 3.6 2.8 - - - +
50H GLU* 2.9 41.2 + - + +
52H LEU* 3.5 25.0 - - + +
74H PHE* 1.3 70.1 - - - +
76H THR* 1.3 64.1 + - - +
77H VAL* 5.4 1.8 - - + -
83H LEU* 5.0 5.8 - - + -
84H CYS 3.5 6.5 - - - +
85H VAL* 4.5 4.0 - - + +
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Residues in contact with THR 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G ALA 4.6 13.2 + - - +
48G GLU* 5.8 1.6 - - - +
51G PHE* 3.8 28.9 - - + -
197G PHE* 4.9 0.2 - - + -
209G LEU* 5.9 1.0 - - - +
48H THR 3.8 2.0 - - - -
49H VAL* 4.0 14.8 - - + +
74H PHE* 4.3 13.2 + - - +
75H ALA* 1.3 77.1 + - - +
77H VAL* 1.3 65.3 + - - +
78H GLN* 3.3 25.0 + - - +
82H GLN 3.6 0.2 - - - +
83H LEU* 3.5 2.3 - - - +
84H CYS* 2.9 37.9 + - - +
86H THR* 5.6 0.9 + - - -
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Residues in contact with VAL 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197G PHE* 3.2 20.4 - - - -
10H LEU* 6.2 1.1 - - + -
41H VAL* 4.8 2.9 - - + -
45H HIS* 4.1 26.9 - - + +
46H VAL 3.8 18.2 - - - +
47H PRO* 3.7 8.7 - - + +
48H THR* 3.3 28.4 + - - +
50H GLU* 6.5 1.3 - - - -
75H ALA* 5.4 0.9 - - + -
76H THR* 1.3 75.2 - - - +
78H GLN* 1.3 73.3 + - - +
79H PRO* 3.6 1.0 - - + -
81H SER* 4.6 11.2 - - - -
82H GLN 3.9 5.8 - - - +
83H LEU* 3.7 25.6 - - + +
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Residues in contact with GLN 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G ALA 5.2 2.5 - - - +
50G LEU* 3.0 52.5 + - + +
51G PHE* 3.3 19.4 + - - +
54G ASN* 3.0 19.8 - - - +
197G PHE* 4.9 0.4 - - - -
76H THR* 3.3 29.6 - - - +
77H VAL* 1.3 74.3 - - - +
79H PRO* 1.3 59.2 - - + +
80H ASP* 3.1 15.0 - - - +
81H SER* 2.7 30.3 + - - -
82H GLN* 2.9 29.0 + - + +
84H CYS* 4.6 10.1 - - - -
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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
------------------------------------------------------------
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