Contacts of the strand formed by residues 78 - 83 (chain Z) 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 Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138X PHE* 2.8 48.2 - - - -
74Z LEU* 4.6 2.8 - - + +
75Z PRO* 3.8 20.2 - - + +
76Z SER 3.3 3.9 - - - -
77Z GLY* 1.3 80.7 - - - +
79Z TYR* 1.3 67.3 + - - +
103Z GLU* 3.5 12.8 + - - +
134Z CYS* 4.4 8.1 - - + -
135Z GLU 3.1 14.6 - - - +
136Z ARG* 3.9 9.6 - - - -
137Z ILE* 4.0 6.7 - - - +
139Z TYR* 3.3 14.4 + - - -
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Residues in contact with TYR 79 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46Y ALA* 3.6 20.6 - - + -
81Y ARG* 2.9 18.3 + - - -
133Y ILE* 3.7 9.4 - - + -
135Y GLU* 2.5 34.1 + - - -
74Z LEU* 4.0 8.7 - - - -
78Z CYS* 1.3 75.9 - - - +
80Z GLY* 1.3 68.0 + - - +
81Z ARG* 3.5 28.3 + - + -
100Z VAL* 3.7 27.4 - - + -
101Z ILE 3.3 12.1 - - - +
102Z ASP* 4.6 2.9 - - - -
103Z GLU 4.8 0.9 - - - +
133Z ILE 3.4 0.7 - - - +
134Z CYS* 3.6 3.8 - - - -
135Z GLU* 2.9 54.9 + - + +
137Z ILE* 3.5 23.3 - - + -
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Residues in contact with GLY 80 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74Z LEU* 3.3 23.1 - - - +
79Z TYR* 1.3 72.4 - - - +
81Z ARG* 1.3 62.1 + - - -
99Z GLY 3.1 2.1 - - - +
101Z ILE* 2.7 46.2 + - - +
132Z LEU* 3.6 13.5 - - - -
133Z ILE 3.3 6.7 - - - -
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Residues in contact with ARG 81 (chain Z).
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* 2.8 21.8 + - - -
81X ARG* 3.6 23.1 - - - +
99X GLY 5.5 0.2 - - - -
100X VAL* 3.7 24.5 - - - +
81Y ARG* 3.5 23.5 - - - +
79Z TYR* 3.5 30.9 + - + +
80Z GLY* 1.3 72.8 - - - +
82Z VAL* 1.3 69.5 + - - +
83Z ALA* 3.4 20.1 + - - +
84Z PRO* 4.4 6.9 - - - +
99Z GLY* 3.2 8.3 - - - +
131Z GLN 3.3 2.6 - - - +
132Z LEU* 3.4 1.2 - - - -
133Z ILE* 2.8 42.2 + - + +
135Z GLU* 2.8 28.1 + - + +
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Residues in contact with VAL 82 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777X DUP 4.4 3.8 - - - +
50Z LEU* 4.1 10.5 - - + -
81Z ARG* 1.3 81.0 + - - +
83Z ALA* 1.3 60.2 + - - +
84Z PRO* 4.7 0.3 - - - +
96Z VAL* 3.6 22.7 - - + +
98Z ALA 5.0 0.3 - - - +
99Z GLY* 2.7 30.1 + - - +
101Z ILE* 3.7 31.9 - - + -
109Z VAL* 4.6 2.2 - - + -
110Z GLY 4.6 5.4 - - - +
111Z VAL* 3.9 15.7 - - + -
130Z ALA* 3.7 26.0 - - + -
131Z GLN 3.4 4.0 - - - +
132Z LEU* 4.3 8.1 - - + -
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Residues in contact with ALA 83 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100X VAL* 3.7 15.7 - - + -
81Z ARG* 3.4 28.9 + - - +
82Z VAL* 1.3 73.8 - - - +
84Z PRO* 1.3 71.3 - - + +
96Z VAL* 3.9 3.8 - - - -
130Z ALA* 3.6 4.7 - - - +
131Z GLN* 2.8 37.2 + - + +
133Z ILE* 3.7 11.9 - - + -
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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