Contacts of the strand formed by residues 78 - 83 (chain X) in PDB entry 3EHW
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 CYS 78 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74X LEU* 4.0 7.9 - - - +
75X PRO* 3.2 48.1 + - - +
77X GLY* 1.3 81.5 + - - +
79X TYR* 1.3 62.9 + - - +
103X GLU* 3.9 11.1 - - - +
134X CYS* 3.7 19.5 - - - -
135X GLU 3.0 24.5 - - - +
137X ILE* 4.1 3.4 - - - -
139X TYR* 3.4 17.5 + - - -
138Y PHE* 3.7 13.5 - - + -
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Residues in contact with TYR 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74X LEU* 3.6 10.8 - - - -
78X CYS* 1.3 74.7 - - - +
80X GLY* 1.3 67.5 + - - +
81X ARG* 3.7 26.5 - - + +
100X VAL* 3.7 28.5 - - + -
101X ILE 3.3 10.8 - - - +
102X ASP* 4.6 2.9 - - - -
103X GLU 4.7 2.0 - - - +
133X ILE 3.3 0.7 - - - +
134X CYS* 3.5 4.3 - - - -
135X GLU* 3.0 54.6 + - + +
137X ILE* 3.5 25.1 - - + -
139X TYR* 4.8 0.4 - - - +
46Z ALA* 3.6 20.4 - - + -
81Z ARG* 2.8 17.8 + - - -
133Z ILE* 3.7 9.6 - - + -
135Z GLU* 2.6 31.6 + - - -
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Residues in contact with GLY 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74X LEU* 3.0 21.9 - - - +
79X TYR* 1.3 74.0 - - - +
81X ARG* 1.3 61.9 + - - -
99X GLY 3.1 1.6 - - - +
101X ILE* 2.7 48.2 + - - +
132X LEU* 3.8 13.0 - - - -
133X ILE 3.3 7.2 - - - -
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Residues in contact with ARG 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79X TYR* 3.7 12.7 + - + +
80X GLY* 1.3 72.4 - - - +
82X VAL* 1.3 70.0 + - - +
83X ALA* 3.4 23.1 + - - +
84X PRO* 4.4 7.9 - - - +
99X GLY* 3.1 9.9 - - - +
131X GLN 3.3 3.1 - - - +
132X LEU* 3.5 2.3 - - - -
133X ILE* 2.8 51.4 + - + +
135X GLU* 2.9 35.0 + - + +
79Y TYR* 2.9 20.2 + - - -
81Y ARG* 3.5 24.3 - - - +
99Y GLY* 5.4 0.8 - - - -
100Y VAL* 3.8 9.9 - - - +
81Z ARG* 3.6 31.0 - - - +
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Residues in contact with VAL 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50X LEU* 4.0 16.4 - - + -
80X GLY 3.7 0.2 + - - -
81X ARG* 1.3 80.1 + - - +
83X ALA* 1.3 60.0 + - - +
84X PRO* 4.6 0.5 - - - +
96X VAL* 3.5 24.3 - - + +
98X ALA 5.1 0.7 - - - +
99X GLY* 2.7 26.9 + - - +
101X ILE* 3.7 32.5 - - + -
109X VAL* 4.6 2.9 - - + -
110X GLY 4.5 5.6 - - - +
111X VAL* 3.9 16.4 - - + -
130X ALA* 3.6 26.7 - - + -
131X GLN 3.4 4.0 - - - -
132X LEU* 4.4 2.7 - - + +
777Y DUP 4.3 4.9 - - - +
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Residues in contact with ALA 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81X ARG* 3.7 17.3 - - - +
82X VAL* 1.3 74.9 - - - +
84X PRO* 1.3 71.8 - - + +
96X VAL* 3.9 3.8 - - - -
130X ALA* 3.5 6.1 - - - +
131X GLN* 2.8 36.4 + - + +
133X ILE* 3.7 30.5 - - + -
100Y VAL* 3.8 9.6 - - + -
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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