Contacts of the strand formed by residues 117 - 122 (chain O) in PDB entry 6CNC
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 THR 117 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75O SER* 3.7 17.2 + - - -
108O GLN* 3.2 4.6 - - - +
109O GLU* 2.9 45.7 + - - +
110O THR* 5.2 2.2 - - - -
111O ALA 5.8 1.3 - - - +
116O LYS* 1.3 77.3 - - - +
118O THR* 1.3 70.4 + - - +
119O TYR* 3.8 33.3 - - + +
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Residues in contact with THR 118 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75O SER* 3.3 18.2 + - - -
76O VAL* 3.2 27.4 + - - +
106O TYR* 4.2 13.7 - - - +
107O LEU 3.4 8.3 - - - -
108O GLN* 3.6 16.4 - - + -
116O LYS* 5.3 8.5 - - - -
117O THR* 1.3 82.2 + - - +
119O TYR* 1.3 70.7 + - - +
120O TYR* 3.8 14.4 - - - +
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Residues in contact with TYR 119 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 5.8 0.9 - - - -
125A HIS* 5.3 8.7 - - - -
73O ARG* 3.0 49.1 - - + -
74O LEU 3.6 3.1 - - - -
75O SER* 3.7 25.6 - - - -
107O LEU* 2.8 44.2 + - + +
108O GLN* 4.5 0.2 - - - +
109O GLU* 3.5 28.7 - - - -
117O THR* 3.8 26.4 + - + +
118O THR* 1.3 82.4 - - - +
120O TYR* 1.3 67.8 + - - +
121O TYR* 4.9 1.1 - - + -
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Residues in contact with TYR 120 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68O LEU* 4.2 17.5 - - + -
73O ARG* 3.3 17.2 - - - +
74O LEU 3.0 21.0 + - - +
75O SER 4.8 0.2 - - - -
76O VAL* 3.3 31.8 - - + +
79O LEU* 5.6 4.5 - - + -
92O LYS* 5.2 2.8 + - - -
95O LEU* 3.1 47.8 - - + +
99O THR* 5.7 0.4 - - - -
104O VAL* 4.5 7.2 - - + -
105O LYS 3.2 11.9 - - - -
106O TYR* 3.3 40.8 - + - -
118O THR* 3.4 21.0 + - - +
119O TYR* 1.3 75.3 - - - +
121O TYR* 1.3 83.7 + - - +
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Residues in contact with TYR 121 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 2.3 37.6 + - - -
68O LEU* 3.2 24.2 - - - +
72O GLY 5.3 1.6 - - - -
73O ARG* 3.1 43.0 - - + +
104O VAL* 3.3 5.0 - - - +
105O LYS* 2.9 37.6 + - + -
106O TYR 5.0 0.2 - - - -
107O LEU* 4.8 17.0 - - + +
119O TYR 4.9 0.2 - - - -
120O TYR* 1.3 93.6 - - - +
122O TYR* 1.3 65.5 + + + +
210O PRO* 3.3 35.4 - - + -
213O ASP* 4.9 0.6 - - + +
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Residues in contact with TYR 122 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A SER* 5.5 2.6 + - - -
237A ALA* 6.5 1.3 - - + -
45O ASP* 5.4 4.1 + - - -
49O TYR* 4.4 24.9 - + + -
65O ILE* 4.6 10.3 - - + -
68O LEU* 3.9 7.9 - - + +
69O VAL* 3.4 58.8 - - + -
72O GLY* 6.5 0.9 - - - -
103O CYS 4.1 5.6 - - - +
105O LYS* 3.8 5.1 - - - +
121O TYR* 1.3 77.5 - + + +
123O ASN* 1.3 67.5 + - - +
124O GLU 3.1 21.9 + - - +
127O ILE* 6.5 1.3 - - + -
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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