Contacts of the strand formed by residues 128 - 138 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A THR* 2.6 51.3 + - - -
162A GLY* 3.4 14.6 + - - -
163A LYS 2.9 10.6 + - - +
164A ASN* 2.7 43.6 + - - +
39B THR* 4.6 2.1 + - - -
41B GLY* 5.1 1.8 - - - -
49B ASP* 3.0 33.5 + - + +
50B LEU 3.2 7.4 - - - +
51B TYR* 3.4 43.7 + - + -
85B ARG* 3.1 36.8 + - - +
88B LEU* 3.9 6.9 - - - +
126B GLY 3.6 0.4 + - - -
127B ASP* 1.3 69.4 - - - +
129B ILE* 1.3 60.7 + - - +
130B ALA 3.6 1.8 - - - -
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU 3.0 11.3 + - - +
51B TYR 5.0 0.4 - - - -
52B SER* 4.2 15.3 - - - +
66B VAL* 4.0 16.6 - - + -
68B THR* 5.7 0.7 - - + -
85B ARG* 4.6 3.5 + - - -
88B LEU* 3.7 25.4 - - + +
94B ILE* 5.1 0.5 - - - +
96B VAL* 4.5 1.9 - - - +
111B VAL* 4.0 31.6 - - + -
113B LEU* 3.5 28.1 - - + +
121B PHE* 4.4 9.4 - - + -
123B VAL* 4.3 18.8 - - + -
127B ASP* 3.8 29.2 - - + +
128B ARG* 1.3 77.5 - - - +
130B ALA* 1.3 66.2 + - - +
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ASP* 3.6 3.3 - - - +
50B LEU* 2.9 24.0 + - + +
82B VAL* 3.7 13.2 - - + -
83B ALA 3.5 12.6 - - - +
85B ARG* 4.1 17.2 - - - +
96B VAL* 4.1 4.0 - - + -
111B VAL* 3.6 32.3 - - + -
128B ARG 3.6 0.8 + - - -
129B ILE* 1.3 80.9 + - - +
131B GLN* 1.3 62.2 + - - +
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Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777A DUP 2.8 37.8 + - - -
45B ALA* 5.7 1.4 - - - +
47B GLY* 3.7 22.2 + - - +
48B TYR 3.3 12.1 - - - +
49B ASP* 3.9 15.1 - - - +
50B LEU* 4.2 5.4 - - - +
81B ARG 3.3 1.4 - - - +
82B VAL* 3.4 2.9 - - - -
83B ALA* 2.7 50.6 + - + +
84B PRO 3.0 20.8 + - - -
85B ARG* 3.9 6.3 - - + +
130B ALA* 1.3 76.7 - - - +
132B LEU* 1.3 59.7 + - - +
133B ILE* 4.6 2.0 - - + -
100C VAL* 3.6 18.9 - - - +
102C ASP* 4.9 1.7 - - - +
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 4.1 24.5 - - + -
38B PRO* 6.2 1.3 - - + -
46B ALA 3.9 0.7 - - - +
47B GLY* 3.2 2.1 - - - -
48B TYR* 2.6 48.2 + - + +
50B LEU* 4.1 20.9 - - + -
70B ILE* 6.1 0.2 - - + -
72B ILE* 3.7 29.8 - - + -
74B LEU* 4.6 5.2 - - + -
80B GLY* 3.8 33.7 - - - +
81B ARG 3.4 6.3 - - - +
82B VAL* 4.2 13.7 - - + -
101B ILE* 4.3 6.5 - - + -
109B VAL* 5.4 1.8 - - + -
131B GLN* 1.3 72.1 - - - +
133B ILE* 1.3 63.0 + - - +
134B CYS* 4.2 3.4 + - - -
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Residues in contact with ILE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ALA 3.5 23.6 - - - +
47B GLY* 3.9 4.0 - - - -
79B TYR 3.2 2.1 - - - +
80B GLY* 3.3 2.6 - - - -
81B ARG* 2.8 67.8 + - - +
83B ALA* 3.8 10.3 - - + -
131B GLN* 4.6 2.5 - - + -
132B LEU* 1.3 76.2 - - - +
134B CYS* 1.3 63.1 + - - +
135B GLU* 3.1 20.5 + - + +
79C TYR* 3.8 12.6 - - + +
100C VAL* 3.7 25.8 - - + -
137C ILE* 3.5 28.3 - - + -
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Residues in contact with CYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 4.6 11.0 - - - -
46B ALA 4.4 3.2 + - - -
48B TYR* 5.8 1.6 - - - -
74B LEU* 4.0 22.9 - - - -
75B PRO* 4.4 4.7 - - - -
78B CYS* 3.8 16.5 - - - +
79B TYR 3.6 5.8 - - - -
132B LEU* 4.2 4.7 + - - -
133B ILE* 1.3 72.3 - - - +
135B GLU* 1.3 62.6 + - - +
136B ARG 3.4 0.3 + - - -
137C ILE* 3.3 7.6 - - - +
138C PHE* 3.1 43.8 + - + +
140C PRO* 3.6 26.7 - - - -
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Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLU* 3.6 9.5 - - - +
78B CYS* 3.0 2.4 - - - -
79B TYR* 3.0 56.1 + - + +
81B ARG* 2.9 40.4 + - + +
133B ILE* 3.7 14.7 - - + +
134B CYS* 1.3 70.5 - - - +
136B ARG* 1.3 62.4 + - - +
137B ILE 3.6 0.5 + - - -
79C TYR* 2.5 38.7 + - - -
81C ARG* 5.1 0.2 - - - -
135C GLU* 3.6 20.0 - - - +
136C ARG 4.0 2.8 - - - +
137C ILE* 3.7 2.4 - - - +
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Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLU* 3.9 2.9 - - - +
136A ARG* 2.9 56.9 + - - +
77B GLY 3.4 7.3 + - - +
78B CYS* 4.1 0.2 - - - -
134B CYS 3.4 0.2 + - - -
135B GLU* 1.3 70.7 - - - +
137B ILE* 1.3 63.1 + - - +
77C GLY 5.7 1.2 + - - -
136C ARG* 2.9 53.1 + - + +
137C ILE 3.8 29.1 + - - +
138C PHE* 3.3 48.8 - - + +
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Residues in contact with ILE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ALA* 3.7 32.8 - - + +
133A ILE* 3.5 21.8 - - + -
134A CYS 3.2 17.0 - - - +
135A GLU* 3.6 4.9 - - - +
136A ARG* 3.8 14.2 + - - +
77B GLY* 3.1 16.1 + - - +
78B CYS* 4.1 10.8 - - - -
79B TYR* 3.5 22.0 - - + +
136B ARG* 1.3 80.3 - - - +
138B PHE* 1.3 65.7 + - - +
139B TYR* 3.5 40.5 + - + +
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Residues in contact with PHE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A MET* 3.3 45.8 - - + -
46A ALA 4.9 3.6 - - - +
75A PRO* 4.5 6.5 - - + -
76A SER 3.8 19.3 - - - -
77A GLY* 4.5 5.6 - - - -
78A CYS* 4.3 12.8 - - + -
134A CYS* 3.1 20.5 + - + +
136A ARG* 3.3 52.5 - - + +
137B ILE* 1.3 85.8 - - - +
139B TYR* 1.3 64.2 + - - +
140B PRO* 3.1 22.7 - - + +
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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