Contacts of the strand formed by residues 82 - 87 (chain B) in PDB entry 3EHU
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 ASN 82 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-307A LYS* 5.3 6.9 - - - +
-304A GLU* 3.1 27.7 + - - +
-303A LYS* 5.3 7.3 + - - +
-300A GLN* 4.0 7.1 + - - +
65B VAL* 3.4 25.7 - - + +
66B ARG 3.4 3.7 - - - +
67B PRO* 3.5 23.2 - - - +
68B CYS* 3.7 7.9 - - - -
79B THR 4.9 0.7 - - - +
80B THR 4.3 9.3 + - - +
81B ASN* 1.3 77.3 - - - +
83B GLY* 1.3 59.9 + - - +
84B TYR* 3.4 27.2 + - + +
98B ASN 4.4 1.6 - - - +
101B GLU* 3.8 19.0 + - - +
102B CYS* 4.1 1.7 - - - -
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Residues in contact with GLY 83 (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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55B TRP* 3.7 11.3 - - - -
65B VAL* 3.4 6.8 - - - +
66B ARG 2.7 34.9 + - - -
67B PRO 4.5 0.2 - - - -
68B CYS* 4.1 4.8 - - - +
82B ASN* 1.3 74.6 - - - +
84B TYR* 1.3 61.9 + - - -
97B VAL* 4.5 0.4 - - - -
98B ASN 3.4 11.2 - - - -
99B TYR* 4.4 17.3 - - - -
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Residues in contact with TYR 84 (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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-304A GLU* 4.1 13.3 + - - -
-8A TYR* 3.5 43.3 - + + +
-5A ARG* 5.2 6.6 + - - -
55B TRP* 3.9 1.7 - - - -
63B LEU* 4.0 20.0 - - + -
64B VAL 3.4 3.8 - - - -
65B VAL* 3.8 32.1 - - + -
82B ASN* 3.4 33.5 + - + +
83B GLY* 1.3 75.7 - - - -
85B ARG* 1.3 61.0 + - - +
96B ARG 4.6 0.5 - - - +
97B VAL* 3.5 3.4 - - - +
98B ASN* 2.9 40.6 + - + +
101B GLU* 3.0 36.8 + - + -
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Residues in contact with ARG 85 (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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47B SER* 4.7 7.7 + - - -
49B ASP* 3.9 14.4 - - - +
55B TRP* 3.4 50.0 - - + +
63B LEU* 4.1 4.2 - - - +
64B VAL* 2.8 38.6 + - - +
84B TYR* 1.3 75.5 - - - +
86B GLU* 1.3 64.1 + - - +
93B TRP* 3.6 42.7 - - + +
94B ALA 2.9 29.6 + - - +
95B ALA* 4.1 11.7 + - - +
96B ARG 4.1 6.9 - - - +
97B VAL* 3.7 22.9 - - + +
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Residues in contact with GLU 86 (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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-14A GLN* 5.9 0.2 - - - +
-11A ALA* 4.3 8.9 - - - +
21A ALA* 3.6 36.6 - - + +
22A GLU* 3.3 32.5 + - - +
61B GLY 3.6 15.8 - - - +
62B GLN 3.7 9.2 - - - -
63B LEU* 3.5 25.6 + - + +
85B ARG* 1.3 74.9 - - - +
87B CYS* 1.3 65.6 + - - +
88B LEU* 3.6 2.4 + - + -
93B TRP* 3.5 6.0 - - - -
94B ALA* 2.9 41.6 + - + +
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Residues in contact with CYS 87 (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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43B GLN 4.2 0.2 - - - -
44B CYS* 2.0 60.8 - - - -
58B SER* 3.6 8.1 - - - -
59B PRO 3.2 26.0 - - - +
60B ALA* 3.6 9.6 - - - -
61B GLY* 2.7 31.4 + - - -
62B GLN 3.0 14.9 + - - +
85B ARG 3.8 1.8 + - - -
86B GLU* 1.3 73.0 - - - +
88B LEU* 1.3 58.3 + - - +
93B TRP* 3.9 13.4 - - + -
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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