Contacts of the helix formed by residues 137 - 150 (chain P) in PDB entry 3HAE
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 ASP 137 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85P TYR* 2.6 35.9 + - - -
121P LYS* 4.5 7.5 + - - -
122P ASP 5.9 0.4 - - - -
123P TYR* 4.6 0.3 - - - -
135P ALA* 3.2 2.7 - - - +
136P ALA* 1.3 83.0 - - + +
138P MET* 1.3 67.4 + - - +
139P ALA 3.2 3.7 + - - -
140P ALA* 3.0 23.7 + - - +
141P GLN* 3.5 22.5 + - - +
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Residues in contact with MET 138 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137P ASP* 1.3 76.2 - - - +
139P ALA* 1.3 67.2 + - - +
141P GLN* 2.8 28.2 + - + +
142P THR* 3.9 2.6 + - - -
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Residues in contact with ALA 139 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84P TYR* 4.4 23.0 - - + +
85P TYR* 3.6 41.1 - - + +
123P TYR* 3.9 8.3 + - + -
137P ASP* 3.2 2.4 + - - -
138P MET* 1.3 77.5 - - - +
140P ALA* 1.3 62.3 + - - +
141P GLN 3.1 1.2 + - - -
142P THR* 3.2 25.6 + - - -
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Residues in contact with ALA 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123P TYR* 3.2 49.0 - - + +
124P ILE* 4.4 3.4 - - + +
135P ALA* 3.5 17.7 - - + +
136P ALA 3.8 1.6 - - - +
137P ASP* 3.0 18.6 + - - +
139P ALA* 1.3 75.9 - - - +
141P GLN* 1.3 58.3 + - - +
143P THR* 3.0 5.6 + - - -
144P LYS* 2.8 27.4 + - - +
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Residues in contact with GLN 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135P ALA* 4.1 12.9 - - - +
137P ASP 3.5 16.7 + - - +
138P MET* 2.8 20.8 + - + +
140P ALA* 1.3 78.4 - - - +
142P THR* 1.3 50.9 + - - +
144P LYS* 3.3 30.5 + - + +
145P HIS* 2.8 35.7 + - - +
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Residues in contact with THR 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84P TYR* 3.6 34.8 - - + +
138P MET 3.9 1.9 + - - -
139P ALA* 3.2 16.5 + - - -
141P GLN* 1.3 74.3 - - - +
143P THR* 1.3 66.4 + - - +
145P HIS* 3.3 7.4 + - - +
146P LYS* 3.0 28.4 + - + +
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Residues in contact with THR 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84P TYR* 3.8 4.5 - - - -
123P TYR* 2.7 33.0 + - + -
124P ILE* 4.5 4.5 - - + -
139P ALA 3.9 0.6 + - - -
140P ALA 3.0 7.0 + - - -
142P THR* 1.3 78.7 - - - +
144P LYS* 1.3 65.4 + - - +
146P LYS* 2.9 8.2 + - - +
147P TRP* 2.8 67.8 + - + +
9R VAL* 3.6 27.1 - - + +
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Residues in contact with LYS 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124P ILE* 4.5 11.7 - - + +
132P SER* 6.2 1.3 - - - -
133P TRP* 3.8 40.0 - - + +
135P ALA* 4.3 13.5 - - + +
140P ALA 2.8 17.2 + - - +
141P GLN* 3.5 33.9 - - + +
143P THR* 1.3 71.5 - - - +
145P HIS* 1.3 64.4 + - - +
147P TRP* 3.8 3.8 - - - +
148P GLU* 2.9 55.4 + - - +
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Residues in contact with HIS 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141P GLN 2.8 21.0 + - - +
142P THR* 3.5 7.9 - - - +
144P LYS* 1.3 73.2 - - - +
146P LYS* 1.3 66.1 + - - +
148P GLU* 3.7 9.0 - - - +
149P ALA* 3.2 25.2 + - + +
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Residues in contact with LYS 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80P THR* 4.8 0.8 - - - +
84P TYR* 3.2 16.8 + - - +
142P THR* 3.0 18.2 + - + +
143P THR* 2.9 11.5 + - - +
145P HIS* 1.3 81.0 + - - +
147P TRP* 1.3 65.7 + - + +
148P GLU 3.0 1.2 + - - -
149P ALA* 3.1 5.9 + - - +
150P ALA* 2.9 30.6 + - + +
7R THR* 6.3 0.4 - - + -
8R GLN 4.3 5.4 - - - -
9R VAL 3.2 35.2 + - - -
27S ARG* 4.0 17.1 - - - +
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Residues in contact with TRP 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97P ARG* 5.2 3.8 - - - -
114P HIS* 4.4 16.6 - + - -
116P TYR* 5.1 5.8 - + - -
124P ILE* 3.4 32.8 - - + -
133P TRP* 3.4 48.2 + + + -
143P THR* 2.8 38.1 + - + +
144P LYS* 4.1 3.1 - - - +
146P LYS* 1.3 79.6 - - + +
148P GLU* 1.3 59.5 + - - +
150P ALA* 3.9 1.6 - - + -
151P HIS* 3.3 0.9 + - - -
152P VAL* 3.0 46.4 + - + +
153P ALA 4.5 0.3 + - - -
7R THR* 3.2 44.2 - - + +
8R GLN 3.0 20.2 + - - -
9R VAL* 4.1 15.5 - - + -
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Residues in contact with GLU 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131P ARG 5.9 2.9 - - - +
132P SER* 5.8 5.2 - - - -
133P TRP* 4.4 17.5 - - + +
144P LYS* 2.9 52.1 + - - +
145P HIS* 3.7 7.6 - - - +
146P LYS 3.1 0.2 - - - -
147P TRP* 1.3 75.4 - - - +
149P ALA* 1.3 66.4 + - - +
151P HIS* 3.0 19.9 + - - -
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Residues in contact with ALA 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145P HIS* 3.2 16.8 + - + +
146P LYS* 3.1 9.6 + - - +
148P GLU* 1.3 79.8 - - - +
150P ALA* 1.3 57.2 + - + +
151P HIS* 3.1 19.1 - - - -
65T LYS* 5.6 1.6 - - - +
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Residues in contact with ALA 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146P LYS* 2.9 17.9 + - + +
147P TRP* 4.5 1.1 - - + -
148P GLU 3.2 0.2 - - - -
149P ALA* 1.3 74.8 - - + +
151P HIS* 1.3 70.9 + - - +
152P VAL* 3.1 21.4 + - + +
155P GLN* 6.0 0.3 + - - -
7R THR* 5.6 3.6 - - + -
96S SER* 5.9 3.1 - - - +
62T ASP* 5.6 5.8 - - - +
65T LYS* 3.6 20.5 + - - +
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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