Contacts of the strand formed by residues 69 - 74 (chain C) in PDB entry 3EGC
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 VAL 69 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67C SER* 3.3 15.7 + - - +
68C ASN* 1.3 83.1 - - - +
70C VAL* 1.3 72.0 + - - +
99C SER* 3.3 11.4 - - - +
101C LEU* 3.9 30.1 - - + -
122C ARG 6.2 0.2 - - - +
123C ARG 5.5 0.2 - - - +
124C VAL* 3.4 13.9 - - + -
125C ASP* 2.9 27.6 + - - +
101D LEU* 4.3 8.7 - - + -
122D ARG* 3.6 26.5 - - - +
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Residues in contact with VAL 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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69C VAL* 1.3 80.0 - - - +
71C GLY* 1.3 73.3 + - - +
72C LEU* 3.8 0.8 + - - +
89C VAL* 5.4 0.7 - - + -
98C TYR* 4.0 15.5 - - + -
99C SER 2.8 11.7 + - - +
100C VAL* 3.7 5.6 - - + -
101C LEU* 3.0 27.0 + - - +
124C VAL* 4.1 3.1 - - - -
126C GLY 3.6 5.4 - - - +
128C ILE* 4.5 2.2 - - + -
308C MET* 3.5 34.1 - - + -
311C LEU* 3.5 28.7 - - + -
312C ILE* 5.9 0.2 - - + -
315C ILE* 3.9 19.1 - - + -
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Residues in contact with GLY 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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70C VAL* 1.3 77.3 - - - +
72C LEU* 1.3 54.7 + - - -
73C ILE 4.0 0.7 - - - -
101C LEU* 3.9 0.9 - - - -
119C PHE* 3.5 26.5 - - - -
124C VAL* 3.8 7.6 - - - +
126C GLY 2.9 10.7 + - - -
127C LEU* 3.3 12.7 - - - -
128C ILE 2.8 31.5 + - - -
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Residues in contact with LEU 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 VAL* 3.8 1.1 + - + -
71C GLY* 1.3 72.3 - - - -
73C ILE* 1.3 61.1 + - - +
74C VAL* 3.9 22.2 - - + -
85C VAL* 5.5 3.4 - - + -
86C ALA* 3.8 34.5 - - + +
89C VAL* 4.2 21.3 - - + -
100C VAL* 3.9 18.2 - - + -
101C LEU 2.8 16.7 + - - +
102C LEU* 3.5 13.0 - - + +
103C ALA 2.9 27.4 + - - +
119C PHE* 3.7 1.8 - - - -
128C ILE* 3.4 35.2 - - + +
130C ALA 5.5 0.7 - - - +
152C VAL* 5.8 0.4 - - + -
102D LEU* 5.1 3.1 - - + -
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Residues in contact with ILE 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 GLY 5.0 0.7 - - - -
72C LEU* 1.3 77.6 - - - +
74C VAL* 1.3 59.8 + - - +
103C ALA* 3.6 5.6 - - + +
105C THR* 3.7 25.6 - - + -
112C GLU* 4.2 4.0 - - + -
115C ALA* 3.7 14.6 - - + -
116C VAL* 3.6 44.4 - - + +
119C PHE* 3.7 23.3 - - + -
127C LEU* 4.3 11.2 - - + -
128C ILE 2.9 10.8 + - - +
129C LEU* 3.5 21.7 - - + -
130C ALA* 2.8 33.3 + - - +
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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 LEU* 3.9 27.4 - - + -
73C ILE* 1.3 77.9 - - - +
75C SER* 1.3 61.0 + - - +
76C ASP 3.4 4.9 + - - +
77C ILE* 3.4 42.6 - - + +
82C PHE* 3.7 27.4 - - + +
85C VAL* 5.6 4.0 - - + -
86C ALA* 5.1 0.7 - - + -
102C LEU* 5.0 2.2 - - + -
103C ALA 3.1 11.5 + - - +
104C ASN* 3.5 3.2 - - - +
105C THR* 3.0 27.8 + - - +
130C ALA* 3.9 14.4 - - + -
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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