Contacts of the helix formed by residues 84 - 95 (chain A) in PDB entry 3WOO
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 84 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A THR* 1.3 85.0 + - - +
85A HIS* 1.3 64.0 + - - +
86A ALA* 3.7 7.0 - - - +
87A CYS* 3.1 13.3 + - - +
88A ALA* 3.0 19.4 + - - +
224A ASP* 3.1 24.6 + - - +
226A ALA 3.9 2.9 - - - -
657A SER* 3.1 17.8 + - - -
658A GLY* 3.0 26.2 + - - +
671A LEU* 3.7 9.2 - - - +
672A ALA 3.1 19.4 + - - +
673A PHE* 3.1 20.3 - - - +
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Residues in contact with HIS 85 (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 ASN* 1.3 69.6 - - - +
86A ALA* 1.3 57.4 + - - +
88A ALA* 3.1 1.8 + - - -
89A TYR* 2.8 60.3 + + - -
92A ILE* 3.7 24.7 - - + +
102A LEU 5.7 0.2 + - - -
103A ILE* 4.7 7.1 + - + +
201A ALA* 5.0 0.2 - - - +
202A PRO* 4.0 22.4 + - + -
204A GLY* 4.1 17.4 + - - -
207A GLY* 3.7 33.7 + - - +
208A LYS* 4.5 6.8 - - + +
224A ASP* 2.7 13.4 + - - +
225A PHE 3.4 28.3 - - - +
226A ALA* 4.0 5.4 - - - -
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASN* 3.2 4.9 - - + +
85A HIS* 1.3 78.5 + - - +
87A CYS* 1.3 59.0 + - - +
89A TYR* 3.4 21.2 - - - +
90A GLY 4.9 0.3 + - - -
224A ASP* 2.9 23.6 + - - +
805A GOL 5.6 0.7 + - - -
1C VAL* 4.3 18.2 - - + -
3C ILE* 3.9 29.4 - - + +
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Residues in contact with CYS 87 (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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67A LEU* 4.4 4.6 - - + +
70A CYS* 2.2 53.5 - - + -
83A THR* 3.3 24.5 - - + +
84A ASN* 3.1 10.4 + - - +
86A ALA* 1.3 77.9 - - - +
88A ALA* 1.3 55.7 + - - +
89A TYR 3.2 2.6 + - - -
228A TYR* 3.7 4.1 + - - -
657A SER* 3.5 27.6 - - - -
805A GOL 2.9 25.6 + - - -
3C ILE* 4.7 0.2 - - - -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A THR* 4.5 2.4 - - + +
84A ASN 3.0 7.2 + - - +
85A HIS 3.1 2.6 + - - +
87A CYS* 1.3 74.8 - - - +
89A TYR* 1.3 64.9 + - - +
90A GLY 3.2 2.7 - - - -
91A ALA* 3.0 4.7 + - - +
92A ILE* 2.9 30.6 + - + +
198A LEU* 4.6 2.7 - - + -
226A ALA* 3.7 29.6 - - + -
228A TYR* 3.4 30.3 - - + +
805A GOL 3.6 1.1 - - - -
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Residues in contact with TYR 89 (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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85A HIS* 2.8 34.0 + + - +
86A ALA* 3.4 20.6 - - - +
87A CYS 3.2 1.6 - - - -
88A ALA* 1.3 77.0 - - - +
90A GLY* 1.3 52.7 + - - +
92A ILE* 3.4 7.0 + - + +
93A GLN* 2.8 36.5 + - + +
103A ILE* 3.6 37.8 - - + +
208A LYS* 4.5 18.8 - - + -
322A ALA* 3.6 31.2 - - + +
323A ALA* 3.8 19.5 - - + -
326A ALA* 4.2 9.0 - - + -
804A GOL 3.0 28.3 + - - -
807A GOL 4.2 2.3 - - - -
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Residues in contact with GLY 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 ALA 4.9 0.4 + - - -
87A CYS 4.5 0.2 + - - -
88A ALA 3.2 0.8 - - - -
89A TYR* 1.3 77.0 - - - +
91A ALA* 1.3 56.9 + - - +
93A GLN* 3.3 1.7 + - - +
94A LEU* 2.8 25.5 + - - +
323A ALA* 4.3 11.8 - - - +
447A ARG* 2.9 29.4 + - - -
805A GOL 3.3 24.0 + - - -
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Residues in contact with ALA 91 (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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88A ALA 3.0 8.5 + - - +
90A GLY* 1.3 75.2 - - - +
92A ILE* 1.3 63.4 + - + +
94A LEU* 3.4 3.6 + - - +
95A ASN* 2.7 33.9 + - - +
118A ALA* 3.6 41.1 - - + +
198A LEU* 4.9 5.8 - - + -
228A TYR* 3.9 13.0 - - + +
805A GOL 3.0 13.9 + - - +
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Residues in contact with ILE 92 (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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85A HIS* 3.7 25.4 - - + +
88A ALA* 3.1 32.3 - - + +
89A TYR* 3.7 7.0 - - + +
91A ALA* 1.3 74.3 - - - +
93A GLN* 1.3 57.8 + - - +
95A ASN* 3.2 12.2 + - - +
96A SER* 2.7 22.7 + - - -
102A LEU* 3.7 16.7 - - + +
103A ILE* 3.6 33.0 - - + +
198A LEU* 4.0 24.0 - - + -
201A ALA* 3.6 26.2 - - + -
226A ALA* 4.8 0.2 - - + -
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Residues in contact with GLN 93 (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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89A TYR* 2.8 19.7 + - + +
90A GLY* 3.5 3.1 - - - +
92A ILE* 1.3 77.0 - - - +
94A LEU* 1.3 63.6 + - - +
96A SER* 3.0 30.0 + - - +
103A ILE* 3.8 20.6 - - + +
319A VAL* 2.9 28.4 - - + +
320A LYS* 3.0 8.4 - - - +
323A ALA* 4.0 20.8 - - + +
446A ARG* 2.8 24.9 + - - +
447A ARG* 2.9 34.7 - - - +
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Residues in contact with LEU 94 (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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90A GLY 2.8 22.7 + - - +
91A ALA* 3.7 6.5 - - - +
92A ILE 3.3 0.4 - - - -
93A GLN* 1.3 75.1 - - - +
95A ASN* 1.3 63.3 + - - +
96A SER 3.3 1.1 + - - +
118A ALA 3.8 17.3 - - - +
119A GLY* 4.0 6.3 - - - -
120A PRO* 5.2 0.2 - - + -
443A GLN* 3.7 56.3 - - + +
446A ARG* 3.7 33.2 + - + +
447A ARG* 3.3 33.0 - - - +
805A GOL 6.2 1.6 - - - +
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Residues in contact with ASN 95 (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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91A ALA 2.7 26.4 + - - +
92A ILE* 3.2 4.6 + - - +
93A GLN 3.1 0.8 - - - -
94A LEU* 1.3 82.8 - - - +
96A SER* 1.3 58.6 + - - +
97A THR* 5.5 1.0 - - - +
100A ASN* 4.3 5.7 + - - +
102A LEU* 3.3 30.0 - - + +
116A VAL* 3.4 30.7 - - + +
117A SER 2.9 25.7 + - - +
118A ALA* 4.3 3.2 - - - +
198A LEU* 5.0 3.0 - - + +
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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