Contacts of the strand formed by residues 68 - 76 (chain C) in PDB entry 2P5V
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 LEU 68 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C LEU 3.3 2.0 - - - -
67C GLY* 1.3 75.7 - - - +
69C GLN* 1.3 61.7 + - - +
113C PHE* 3.5 4.0 - - - -
114C PHE* 2.9 46.0 + - + +
115C THR 3.9 0.8 + - - +
116C ASP* 3.5 38.1 - - - +
117C MSE 3.5 14.8 - - + +
120C PHE* 3.6 21.8 - - + -
141C PHE* 3.5 29.8 - - + -
117F MSE 3.7 36.8 - - + -
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Residues in contact with GLN 69 (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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61C PRO* 5.7 0.3 - - - +
67C GLY 4.0 3.0 + - - +
68C LEU* 1.3 75.6 - - - +
70C ALA* 1.3 63.0 + - - +
71C PHE* 4.4 3.0 - - + -
111C GLN* 2.9 32.1 - - - +
112C ALA 3.6 7.6 - - - +
113C PHE* 3.3 34.2 - - + -
141C PHE* 3.3 6.6 - - - +
142C VAL* 3.0 59.4 + - + +
145C GLU* 5.0 4.0 - - - +
148C HIS* 6.3 0.6 - - - -
100D PHE* 3.6 26.2 - - - -
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Residues in contact with ALA 70 (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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68C LEU* 4.1 0.6 - - + -
69C GLN* 1.3 74.4 - - - +
71C PHE* 1.3 63.4 + - - +
72C ILE* 3.9 9.0 - - + -
110C LEU 3.7 0.3 - - - +
111C GLN* 3.4 8.3 - - - +
112C ALA* 2.9 36.1 + - - +
114C PHE* 4.2 5.6 - - + -
120C PHE* 3.4 35.4 - - + -
139C SER* 5.0 0.4 - - - -
140C SER 3.4 4.7 - - - +
141C PHE* 3.7 11.9 - - + -
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Residues in contact with PHE 71 (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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69C GLN* 4.4 2.9 - - + -
70C ALA* 1.3 74.2 - - - +
72C ILE* 1.3 62.4 + - - +
73C ARG* 3.9 1.6 + - - +
109C LEU* 4.2 20.4 - - + -
110C LEU 3.3 5.6 - - - -
111C GLN* 3.8 31.6 - - + -
139C SER* 3.3 2.6 - - - -
140C SER* 2.8 36.6 + - - +
142C VAL* 4.1 11.9 - - + -
71D PHE* 4.9 7.4 - + - -
100D PHE* 3.6 38.8 - + - -
102D LEU* 3.8 25.4 - - + -
109D LEU* 3.3 28.7 - - + -
111D GLN* 5.7 0.4 - - - -
903D GOL 3.7 18.2 + - - +
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Residues in contact with ILE 72 (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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70C ALA* 4.2 5.6 - - + +
71C PHE* 1.3 73.1 - - - +
73C ARG* 1.3 62.5 + - - +
74C VAL* 3.6 11.0 + - + +
108C TYR 3.5 3.6 - - - +
109C LEU* 3.5 1.8 - - - -
110C LEU* 2.8 56.2 + - + +
112C ALA* 4.4 14.8 - - + -
120C PHE* 4.0 21.3 - - + -
123C PHE* 3.7 29.4 - - + -
124C VAL* 5.1 0.4 - - + -
128C LEU* 3.7 26.0 - - + -
137C ALA* 3.9 9.4 - - + -
138C GLN 3.7 2.5 - - - +
139C SER* 3.5 20.9 - - - +
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Residues in contact with ARG 73 (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 4.9 0.6 + - - +
72C ILE* 1.3 71.5 - - - +
74C VAL* 1.3 61.9 + - - +
75C SER 4.0 0.3 + - - -
106C THR* 3.4 32.3 - - + +
108C TYR 3.5 4.5 - - - -
109C LEU* 3.8 17.0 - - + -
137C ALA* 3.3 4.6 - - - -
138C GLN* 2.7 76.5 + - + +
139C SER* 3.8 16.2 + - - +
140C SER* 3.5 22.9 + - - -
73D ARG* 4.5 5.7 - - - +
104D GLY* 6.0 1.0 - - - -
105D GLU* 5.8 6.3 - - - +
106D THR* 5.6 1.6 + - - +
903D GOL 3.7 29.6 + - - +
104E GLY* 5.4 2.0 - - - -
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Residues in contact with VAL 74 (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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72C ILE* 3.8 20.9 - - + +
73C ARG* 1.3 75.1 - - - +
75C SER* 1.3 73.3 + - - +
76C ILE* 4.6 2.9 - - + +
86C PHE* 4.1 17.9 - - + -
106C THR* 4.1 1.1 - - - +
107C ASP* 3.3 10.8 + - - +
108C TYR* 2.8 44.6 + - + +
110C LEU* 4.0 25.6 - - + -
128C LEU* 4.2 10.3 - - + -
134C VAL* 4.0 16.6 - - + -
136C ASP 3.7 7.6 - - - +
137C ALA* 4.2 2.7 - - + -
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Residues in contact with SER 75 (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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73C ARG 4.0 1.2 + - - -
74C VAL* 1.3 78.6 - - - +
76C ILE* 1.3 61.3 + - - +
78C LYS* 4.9 2.3 + - - -
105C GLU 6.1 0.2 - - - -
107C ASP* 3.4 11.7 + - - +
134C VAL 3.8 0.2 - - - -
135C GLN* 2.9 59.0 + - - -
136C ASP* 2.8 23.5 + - - +
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Residues in contact with ILE 76 (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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74C VAL* 4.0 2.8 + - + -
75C SER* 1.3 75.5 - - - +
77C ARG* 1.3 75.9 + - - +
78C LYS* 3.3 24.6 + - - +
82C ALA* 3.8 11.9 - - + +
83C ARG* 4.1 32.1 - - + +
86C PHE* 3.5 44.0 - - + -
107C ASP* 2.8 18.3 + - - +
108C TYR* 3.9 16.8 - - + -
133C GLY 3.2 21.1 - - - +
134C VAL* 4.9 1.6 - - - -
135C GLN* 3.6 9.9 - - - +
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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