Contacts of the helix formed by residues 85 - 90 (chain A) in PDB entry 3WF4
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 PRO 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A TYR* 3.4 15.5 - - + +
58A SER* 3.7 25.1 - - - +
83A TYR* 3.4 10.5 - - + +
84A VAL* 1.3 80.9 - - - +
86A TRP* 1.3 67.8 + - - +
87A ASN* 3.2 2.7 - - - +
88A PHE* 2.9 27.1 + - + +
89A HIS* 3.3 11.2 - - - +
126A ILE* 3.9 24.7 - - + -
130A TRP* 3.7 27.8 - - + +
134A GLY* 4.6 2.7 - - - -
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Residues in contact with TRP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A VAL 3.4 6.0 + - - +
85A PRO* 1.3 68.9 - - - +
87A ASN* 1.3 57.1 + - - +
89A HIS* 2.8 20.6 + - - +
90A GLU* 2.9 38.9 + - + +
124A PRO* 3.9 19.8 + - + +
134A GLY 3.3 9.6 + - - +
135A LEU* 3.9 22.2 - - + -
136A PRO* 3.4 27.6 - - + +
138A TRP* 3.9 17.0 - + - -
139A LEU* 4.0 12.1 - - + -
154A TYR* 4.7 0.2 - + - -
157A ALA* 3.6 24.7 - - + -
158A VAL* 3.7 40.6 - - + -
161A TRP* 3.3 48.7 - + + +
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Residues in contact with ASN 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PRO* 3.9 2.1 - - - +
86A TRP* 1.3 72.6 - - - +
88A PHE* 1.3 68.5 + - - +
89A HIS 3.2 0.7 + - - -
90A GLU 4.2 3.6 - - - -
91A PRO* 4.0 19.0 - - + +
130A TRP* 2.8 26.7 + - - +
131A GLU* 2.8 39.6 + - - +
134A GLY* 2.9 27.7 + - - +
135A LEU 3.6 5.1 + - - -
136A PRO* 3.8 23.5 - - + +
317A TRP* 3.6 16.1 - - - -
413A TYR* 3.6 15.9 + - - +
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Residues in contact with PHE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A TYR* 4.0 6.7 - + - -
58A SER* 3.7 37.7 - - - -
85A PRO* 2.9 25.2 + - + +
87A ASN* 1.3 81.4 + - - +
89A HIS* 1.3 73.6 + - - +
91A PRO* 5.3 0.2 - - - -
97A GLN* 3.3 9.6 - - - +
101A ASP* 3.5 28.3 - - + -
102A HIS* 3.0 63.4 + + - -
130A TRP* 3.9 13.0 - + + -
317A TRP* 3.7 34.6 - + - -
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Residues in contact with HIS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 2.6 33.6 + + - -
84A VAL* 3.7 15.8 - - + +
85A PRO* 3.3 21.8 - - + -
86A TRP 2.8 3.0 + - - +
88A PHE* 1.3 91.7 + + - +
90A GLU* 1.3 59.2 + - - +
91A PRO* 3.7 4.5 - - - -
96A TYR* 3.1 11.5 - - - +
97A GLN 2.8 46.2 + - - +
98A PHE* 3.9 8.1 - + + -
102A HIS 3.0 27.8 + - - -
104A VAL* 4.0 11.3 - - + +
161A TRP* 3.4 24.5 - + + -
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A TRP* 2.9 39.2 + - + +
87A ASN 4.3 2.5 - - - -
89A HIS* 1.3 77.9 - - - +
91A PRO* 1.3 63.4 - - - +
92A TRP 3.3 15.0 - - - +
93A PRO* 3.5 4.7 - - - +
94A GLY 2.8 21.8 + - - +
95A GLN 3.4 2.7 - - - +
96A TYR* 3.1 34.0 + - + -
136A PRO* 4.1 6.6 - - - +
138A TRP* 2.9 37.3 + - + -
157A ALA 5.3 0.2 - - - +
160A LYS* 4.7 6.1 - - - +
161A TRP* 4.0 11.4 + - + +
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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