Contacts of the helix formed by residues 89 - 97 (chain A) in PDB entry 3ANX
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 GLY 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A GLY 3.5 6.7 + - - -
87A GLY 3.1 5.1 + - - -
88A GLU* 1.3 77.6 - - - +
90A ALA* 1.3 58.6 + - - +
91A THR 3.7 1.3 - - - -
92A LEU* 3.3 15.3 - - - +
93A ARG* 2.9 23.4 + - - +
106A MET* 4.9 1.6 - - - -
125A HIS* 3.8 9.7 - - - -
128A ALA* 3.7 7.9 - - - +
129A PHE* 3.9 19.5 - - - -
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Residues in contact with ALA 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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60A GLU* 3.6 1.1 - - - +
64A HIS* 3.2 41.3 - - + +
86A GLY 4.7 0.6 + - - -
88A GLU* 3.3 5.9 + - - +
89A GLY* 1.3 72.9 - - - +
91A THR* 1.3 69.5 + - - +
92A LEU 3.2 1.3 - - - -
93A ARG* 2.8 37.5 + - - +
94A GLU* 2.8 17.7 + - - +
124A TRP* 4.3 7.4 - - + -
125A HIS 4.5 0.8 - - - +
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Residues in contact with THR 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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64A HIS* 3.7 13.3 + - - -
67A LEU* 3.9 6.8 - - + +
68A VAL* 3.9 19.5 - - + +
83A ILE* 3.9 27.8 - - + -
86A GLY* 4.2 10.5 + - - -
89A GLY* 3.7 0.4 - - - -
90A ALA* 1.3 74.7 - - - +
92A LEU* 1.3 52.7 + - - +
94A GLU* 3.1 1.7 + - - +
95A VAL* 2.6 40.0 + - + +
156A ILE* 3.9 27.8 - - + -
158A ASP* 3.4 21.8 + - + -
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Residues in contact with LEU 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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83A ILE* 3.6 17.7 - - + +
86A GLY 5.5 0.2 + - - -
89A GLY* 3.3 16.2 + - - +
91A THR* 1.3 76.8 - - - +
93A ARG* 1.3 67.1 + - - +
95A VAL* 2.8 11.5 + - + -
96A LEU* 2.8 38.1 + - + +
104A ALA* 4.1 22.4 - - + +
106A MET* 3.9 29.2 - - + -
128A ALA* 4.0 13.2 - - + -
129A PHE* 4.3 21.3 - - + +
134A ALA* 4.3 16.2 - - + -
135A VAL 5.8 0.2 - - - +
136A LEU 6.3 0.4 - - - +
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Residues in contact with ARG 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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60A GLU* 2.8 44.2 + - - -
61A TYR* 4.3 12.1 - - - +
64A HIS* 4.5 1.2 + - - -
89A GLY 2.9 14.6 + - - +
90A ALA* 2.8 21.3 + - - +
92A LEU* 1.3 76.0 - - - +
94A GLU* 1.3 89.1 + - - +
96A LEU* 3.2 6.3 + - - +
97A LYS* 3.2 28.4 + - + +
123A GLU 3.6 3.0 + - - -
124A TRP* 2.4 41.5 + - - +
125A HIS 4.1 8.5 - - - +
126A GLN* 3.7 32.6 + - + +
128A ALA* 4.5 7.9 - - + +
265A ARG* 5.8 1.0 - - - +
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Residues in contact with GLU 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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61A TYR* 5.3 2.0 - - - +
64A HIS* 3.9 22.4 - - + +
65A GLU* 3.7 12.2 - - - +
68A VAL* 4.1 12.1 - - + -
69A HIS* 2.9 28.2 + - + +
90A ALA 2.8 15.9 + - - +
91A THR 4.1 1.3 - - - +
93A ARG* 1.3 107.6 + - - +
95A VAL* 1.3 67.3 + - - +
97A LYS* 2.8 49.8 + - - +
98A HIS* 3.7 10.0 - - - -
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Residues in contact with VAL 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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68A VAL* 3.4 23.1 - - + -
72A MET* 3.7 20.4 - - + -
81A VAL* 3.7 30.5 - - + -
83A ILE* 3.8 23.1 - - + -
91A THR* 2.6 29.2 + - + +
92A LEU* 2.8 7.8 + - + +
94A GLU* 1.3 74.5 - - - +
96A LEU* 1.3 63.0 + - - +
98A HIS* 3.0 14.9 + - - -
101A VAL* 3.9 15.2 - - + +
104A ALA* 4.7 4.7 - - + -
156A ILE* 4.5 5.6 - - + -
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Residues in contact with LEU 96 (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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92A LEU* 2.8 38.5 + - + +
93A ARG* 3.7 5.2 - - - +
95A VAL* 1.3 71.6 - - - +
97A LYS* 1.3 60.0 + - - +
98A HIS 3.0 2.1 + - - -
101A VAL* 4.6 4.9 - - + -
104A ALA* 3.8 25.6 - - + -
128A ALA* 3.8 13.2 - - - +
131A ASP* 3.6 33.2 - - + +
133A ARG* 2.9 59.6 + - + +
134A ALA* 4.4 4.0 - - + -
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Residues in contact with LYS 97 (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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65A GLU* 4.4 7.1 + - - -
69A HIS* 4.3 6.3 - - + -
93A ARG* 3.2 21.9 + - + +
94A GLU* 2.8 51.7 + - - +
95A VAL 3.1 1.0 + - - -
96A LEU* 1.3 74.0 - - - +
98A HIS* 1.3 58.8 + - - +
99A PRO* 3.8 6.1 - - - +
260A ARG 4.4 3.6 - - - +
261A ASN 4.6 3.9 - - - +
262A LEU* 3.8 20.8 - - + +
263A ALA* 3.0 36.6 + - + +
265A ARG* 5.9 4.4 - - - +
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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