Contacts of the strand formed by residues 111 - 117 (chain C) in PDB entry 7CE1
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 111 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67C ARG* 3.1 48.8 + - - +
78C ASN 3.1 7.2 + - - +
79C VAL* 3.7 7.0 - - + -
80C ILE* 2.9 27.9 + - - +
105C LEU* 4.6 2.7 - - - -
109C GLN 4.4 3.2 + - - -
110C TYR* 1.3 81.9 - - - +
112C LEU* 1.3 61.9 + - - +
113C VAL* 3.9 0.4 + - + -
113D VAL* 4.9 17.9 - - + +
115D THR* 4.6 16.5 - - + +
129D TYR* 2.9 40.0 + + - -
135D SER* 4.0 14.8 - - - -
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Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ILE* 3.5 33.9 - - + +
82C LEU* 4.1 27.8 - - + -
98C VAL* 3.8 13.7 - - + +
101C ILE* 4.1 20.9 - - + -
102C THR* 3.7 25.1 - - + -
105C LEU* 4.0 10.5 - - + +
111C HIS* 1.3 76.7 - - - +
113C VAL* 1.3 65.3 + - - +
114C VAL* 5.1 1.3 - - + -
112D LEU 3.9 0.2 - - - +
113D VAL* 3.2 4.1 - - - +
114D VAL* 3.0 51.6 + - + +
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Residues in contact with VAL 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C VAL* 3.5 29.8 - - + -
80C ILE 3.1 13.3 + - - +
81C ALA* 3.8 15.5 - - + -
82C LEU* 3.1 28.9 + - - +
111C HIS 3.9 0.9 + - - -
112C LEU* 1.3 75.6 - - - +
114C VAL* 1.3 63.3 + - - +
115C THR* 4.4 9.2 - - - +
135C SER 5.5 1.3 - - - +
111D HIS* 5.2 17.0 - - + -
112D LEU 3.2 10.3 - - - +
113D VAL* 3.5 24.2 - - + -
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Residues in contact with VAL 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C LEU* 3.6 18.8 - - + +
84C LEU* 4.7 20.0 - - + -
98C VAL* 5.6 4.5 - - + -
112C LEU* 5.1 2.2 - - + -
113C VAL* 1.3 76.4 - - - +
115C THR* 1.3 72.4 + - - +
116C PRO* 4.0 12.6 - - + +
98D VAL* 4.3 21.5 - - + -
99D PHE* 5.7 1.6 - - + -
102D THR* 5.1 3.6 - - + +
112D LEU* 3.0 30.1 + - + +
114D VAL* 4.1 31.6 - - + -
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Residues in contact with THR 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ALA* 4.9 5.5 - - - +
82C LEU 3.0 9.6 + - - -
83C VAL* 3.1 38.0 - - - +
84C LEU 3.2 1.9 + - - -
113C VAL* 4.1 12.3 + - - +
114C VAL* 1.3 77.4 + - - +
116C PRO* 1.3 69.6 - - + +
117C HIS 4.1 0.2 + - - -
126C PRO* 3.7 25.8 - - + +
129C TYR* 5.3 12.4 - - + -
130C ILE* 5.0 5.5 - - + +
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Residues in contact with PRO 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C LEU* 3.1 17.3 - - + +
86C VAL* 4.0 18.2 - - + -
114C VAL* 4.0 6.3 - - + +
115C THR* 1.3 95.7 - - + +
117C HIS* 1.3 60.9 + - - +
118C THR* 5.7 1.4 - - + +
126C PRO* 5.4 1.8 - - - +
99D PHE* 4.4 11.9 - - + -
102D THR* 3.5 43.5 - - + +
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Residues in contact with HIS 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C VAL* 5.2 6.7 - - + +
84C LEU 3.3 10.9 + - - -
85C SER* 3.7 35.3 + - - -
86C VAL* 3.3 21.5 + - - +
116C PRO* 1.3 76.0 - - - +
118C THR* 1.3 63.6 + - - +
119C HIS 3.8 21.5 + - - -
120C ALA* 4.6 2.7 - - - -
122C ASP* 3.3 25.7 + - + +
123C SER* 4.0 27.2 + - - -
125C VAL* 5.5 0.4 - - + -
126C PRO* 4.2 20.6 - - + -
150C ARG* 5.0 7.0 + - - -
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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