Contacts of the strand formed by residues 107 - 112 (chain C) in PDB entry 2VUU
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 107 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75C HIS 3.4 2.0 + - - -
76C LEU* 3.5 20.5 - - + -
77C ALA 3.1 23.2 + - - -
105C ILE* 3.6 3.0 - - - +
106C GLN* 1.3 80.6 - - - +
108C TYR* 1.3 62.9 + - - +
109C ILE* 3.9 6.9 - - + +
144C PRO 3.5 8.7 - - - -
145C SER* 4.4 5.8 - - - -
146C THR* 3.0 27.6 + - - -
203C ILE* 3.5 30.0 + - + +
204C PHE* 3.5 21.7 + + + -
207C GLY* 3.3 33.2 + - - -
208C PRO* 3.9 17.1 - - + +
211C TRP* 4.4 0.6 - - + -
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Residues in contact with TYR 108 (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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71C PHE* 4.4 5.8 - + - -
77C ALA* 3.8 13.0 - - + -
79C ILE* 3.4 35.8 - - + +
92C GLY* 4.5 2.4 + - - -
95C LEU* 3.8 7.8 - - - +
96C ALA* 3.7 23.1 + - - +
99C ALA* 3.5 32.5 - - + -
105C ILE* 4.0 10.1 - - + +
107C HIS* 1.3 72.9 - - - +
109C ILE* 1.3 63.0 + - - +
110C TYR* 3.7 23.0 + + + -
134C VAL* 6.0 0.2 - - - +
138C VAL* 4.1 22.9 - - + +
143C LEU* 4.0 17.7 - - + -
144C PRO 2.7 15.8 + - - +
145C SER* 3.0 30.1 - - - -
146C THR 3.3 1.0 + - - +
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Residues in contact with ILE 109 (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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77C ALA 2.9 13.2 + - - +
78C PHE* 3.4 7.9 - - + -
79C ILE* 2.8 27.4 + - - +
107C HIS* 4.4 8.1 - - - +
108C TYR* 1.3 73.2 - - - +
110C TYR* 1.3 68.5 + - - +
146C THR* 3.2 15.7 - - - +
148C VAL* 4.0 26.0 - - + -
200C LEU* 4.2 17.0 - - + +
203C ILE* 3.6 34.3 - - + -
204C PHE* 3.2 42.2 - - + -
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Residues in contact with TYR 110 (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 ILE* 3.4 32.3 - - + -
81C THR* 4.2 15.8 + - + -
88C GLU* 5.0 1.7 + - - +
92C GLY* 5.2 4.0 - - - -
108C TYR* 3.7 17.8 + + + -
109C ILE* 1.3 77.2 - - - +
111C SER* 1.3 76.9 + - - +
112C SER* 3.5 18.7 + - - -
131C LYS* 3.3 43.7 - - - +
134C VAL* 3.4 32.5 - - + +
135C GLU* 4.1 3.6 - - - -
138C VAL* 4.9 1.3 - - + -
146C THR 3.1 5.5 + - - -
147C PHE* 3.3 31.9 - + + -
148C VAL* 3.1 22.5 + - - +
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Residues in contact with SER 111 (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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17C GLN* 3.2 26.7 + - - -
78C PHE* 4.0 10.2 - - - -
79C ILE 2.9 8.9 + - - +
80C ASN* 3.4 29.9 + - - +
109C ILE 4.2 0.2 - - - -
110C TYR* 1.3 86.8 - - - +
112C SER* 1.3 60.6 + - - +
131C LYS* 3.7 11.2 + - - +
148C VAL* 3.5 18.0 + - - +
150C ALA* 4.9 4.9 + - - +
218C LEU* 5.9 0.3 - - - +
1353C NAP 5.9 0.5 - - - -
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Residues in contact with SER 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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110C TYR* 3.5 23.9 + - - -
111C SER* 1.3 76.4 + - - +
113C MET* 1.3 82.4 + - - +
131C LYS* 3.9 6.5 - - - -
135C GLU* 2.9 30.2 + - - -
147C PHE* 3.7 5.7 - - - +
148C VAL 2.8 18.4 + - - +
149C TYR* 3.2 26.3 - - - -
150C ALA 4.4 0.9 + - - -
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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