Contacts of the strand formed by residues 128 - 138 (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 ARG 128 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161Y THR* 2.8 45.1 + - - -
162Y GLY* 3.1 19.8 + - - -
163Y LYS* 2.8 11.4 + - - +
164Y ASN* 2.8 30.8 + - - +
39Z THR* 4.2 2.5 - - - -
41Z GLY* 5.2 2.0 - - - -
49Z ASP* 2.9 43.5 + - + -
50Z LEU 3.3 7.4 - - - +
51Z TYR* 3.5 39.1 + - + -
85Z ARG* 3.1 39.6 + - - +
88Z LEU* 3.8 6.9 - - - +
127Z ASP* 1.3 68.0 - - - +
129Z ILE* 1.3 60.4 + - - +
130Z ALA 3.6 2.0 - - - -
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Residues in contact with ILE 129 (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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50Z LEU 3.0 11.0 + - - +
51Z TYR 4.9 0.7 - - - -
52Z SER* 4.1 16.6 - - - +
66Z VAL* 4.1 12.8 - - + -
68Z THR* 5.6 0.7 - - + -
85Z ARG* 4.6 2.7 + - - -
88Z LEU* 3.8 23.7 - - + +
94Z ILE* 5.2 0.5 - - - +
96Z VAL* 4.6 2.1 - - - +
111Z VAL* 3.7 35.7 - - + -
113Z LEU* 3.6 26.6 - - + +
121Z PHE* 4.8 7.4 - - + -
123Z VAL* 3.9 21.1 - - + -
127Z ASP* 3.7 30.1 - - + +
128Z ARG* 1.3 77.9 - - - +
130Z ALA* 1.3 66.9 + - - +
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Residues in contact with ALA 130 (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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49Z ASP* 3.5 6.1 - - - +
50Z LEU* 2.8 24.5 + - + +
82Z VAL* 3.7 22.2 - - + -
83Z ALA 3.6 13.5 - - - +
85Z ARG* 4.0 15.9 - - - +
96Z VAL* 4.2 4.9 - - + -
111Z VAL* 3.7 20.0 - - + -
128Z ARG 3.6 1.0 + - - -
129Z ILE* 1.3 80.3 + - + +
131Z GLN* 1.3 65.3 + - - +
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Residues in contact with GLN 131 (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 20.4 - - - +
102X ASP* 5.0 1.2 - - - +
777Y DUP 2.7 38.3 + - - -
45Z ALA* 5.8 1.6 - - - +
47Z GLY* 3.7 22.7 + - - +
48Z TYR 3.3 9.2 - - - +
49Z ASP* 3.7 18.2 - - - +
50Z LEU* 4.2 4.9 - - - +
81Z ARG 3.3 1.2 - - - +
82Z VAL* 3.4 2.6 - - - -
83Z ALA* 2.8 45.0 + - + +
84Z PRO 3.1 20.0 + - - -
85Z ARG* 4.0 6.6 - - + +
130Z ALA* 1.3 78.6 - - - +
132Z LEU* 1.3 60.1 + - - +
133Z ILE* 4.5 2.0 - - + -
165Z MG 4.3 0.5 - - - -
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Residues in contact with LEU 132 (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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26Z LEU* 4.1 26.7 - - + -
38Z PRO* 6.0 1.1 - - + -
40Z ARG* 5.2 0.2 + - - -
46Z ALA 4.0 0.5 - - - +
47Z GLY* 3.4 0.9 - - - -
48Z TYR* 2.7 46.2 + - + +
50Z LEU* 4.0 22.7 - - + -
70Z ILE* 5.9 0.2 - - + -
72Z ILE* 3.6 29.6 - - + -
74Z LEU* 4.6 2.7 - - + -
80Z GLY* 3.6 35.4 - - - +
81Z ARG 3.4 5.2 - - - +
82Z VAL* 4.3 7.0 - - + -
101Z ILE* 4.2 13.7 - - + -
109Z VAL* 5.2 1.8 - - + -
131Z GLN* 1.3 73.7 - - - +
133Z ILE* 1.3 63.3 + - - +
134Z CYS* 4.1 3.7 + - - -
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Residues in contact with ILE 133 (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* 3.7 11.0 - - + +
100X VAL* 3.6 40.4 - - + -
137X ILE* 3.5 28.0 - - + -
46Z ALA* 3.8 19.5 - - + +
47Z GLY* 4.0 7.9 - - - -
80Z GLY* 3.3 4.4 - - - -
81Z ARG* 2.8 52.5 + - - +
83Z ALA* 3.7 9.0 - - + -
131Z GLN* 4.5 3.4 - - + -
132Z LEU* 1.3 76.7 - - - +
134Z CYS* 1.3 62.6 + - - +
135Z GLU* 3.2 18.6 + - + +
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Residues in contact with CYS 134 (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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137X ILE* 3.2 8.6 - - - +
138X PHE* 3.1 44.4 + - + +
140X PRO* 3.5 30.3 - - + -
26Z LEU* 4.6 10.3 - - - -
40Z ARG* 5.7 0.2 - - - -
46Z ALA 4.5 3.2 + - - -
48Z TYR* 5.6 1.8 - - - -
74Z LEU* 4.0 22.4 - - - -
75Z PRO* 4.5 8.1 - - + -
78Z CYS* 4.4 8.3 - - + -
79Z TYR 3.6 6.1 - - - -
132Z LEU* 4.1 4.9 + - - -
133Z ILE* 1.3 71.7 - - - +
135Z GLU* 1.3 61.3 + - - +
136Z ARG* 4.4 0.9 - - - +
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Residues in contact with GLU 135 (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* 2.6 38.9 + - - -
135X GLU* 3.6 15.5 - - - +
136X ARG 4.2 1.6 - - - +
137X ILE* 3.6 4.1 - - - +
135Y GLU* 3.6 13.0 - - - +
78Z CYS* 3.1 4.5 - - - -
79Z TYR* 2.9 53.6 + - + -
81Z ARG* 2.8 42.2 + - + -
133Z ILE* 3.7 14.8 - - + +
134Z CYS* 1.3 71.1 - - - +
136Z ARG* 1.3 62.4 + - - +
137Z ILE 3.6 0.2 + - - -
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Residues in contact with ARG 136 (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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77X GLY* 5.6 1.8 + - - -
136X ARG* 3.0 51.2 + - - +
137X ILE 3.8 24.3 + - - +
138X PHE* 3.3 39.8 - - + +
135Y GLU* 3.8 2.6 - - - +
136Y ARG* 2.9 67.1 + - + +
77Z GLY 3.5 7.7 + - - +
78Z CYS* 3.9 16.6 - - - -
135Z GLU* 1.3 71.6 - - - +
137Z ILE* 1.3 64.5 + - - +
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Residues in contact with ILE 137 (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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46Y ALA* 3.7 33.7 - - + +
133Y ILE* 3.5 25.1 - - + -
134Y CYS 3.2 11.0 - - - +
135Y GLU* 3.8 4.0 - - - +
136Y ARG* 3.8 14.5 + - - -
77Z GLY* 3.0 25.8 + - - +
78Z CYS* 4.0 10.8 - - - -
79Z TYR* 3.5 20.9 - - + -
136Z ARG* 1.3 81.9 - - - +
138Z PHE* 1.3 65.5 - - - +
139Z TYR* 3.5 36.2 + - + +
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Residues in contact with PHE 138 (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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46Y ALA 5.0 2.8 - - - +
75Y PRO* 4.2 12.1 - - + -
76Y SER 3.4 26.7 - - - -
77Y GLY* 4.1 7.4 - - - -
78Y CYS* 3.8 32.5 - - + -
134Y CYS* 3.0 19.0 + - + +
136Y ARG* 3.3 43.7 - - + +
137Z ILE* 1.3 82.3 - - - +
139Z TYR* 1.3 66.0 + - - +
140Z PRO* 3.3 22.3 - - + +
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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