Contacts of the helix formed by residues 134 - 153 (chain V) in PDB entry 2AXT
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 THR 134 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121V LEU* 6.1 0.9 - - - -
132V ASN 3.4 9.9 - - - +
133V LEU* 1.3 77.0 - - - +
135V GLU* 1.3 53.9 + - - +
136V LYS* 2.6 23.8 + - - +
137V ASP* 2.5 53.1 + - - +
138V LEU* 2.9 13.2 + - - -
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Residues in contact with GLU 135 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99V VAL* 3.6 14.9 - - - +
103V LYS* 2.9 43.4 + - - -
121V LEU* 5.2 3.6 - - - +
134V THR* 1.3 72.6 - - - +
136V LYS* 1.3 57.6 + - - +
138V LEU* 3.8 10.8 + - - +
139V VAL* 2.9 33.0 + - + +
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Residues in contact with LYS 136 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51V GLN* 5.7 3.9 + - - +
134V THR* 2.6 16.4 + - - +
135V GLU* 1.3 74.8 - - - +
137V ASP* 1.3 75.1 + - - +
139V VAL* 3.1 22.5 + - - +
140V ALA* 3.3 6.4 + - - +
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Residues in contact with ASP 137 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57V ARG* 5.7 0.9 + - - -
58V LEU* 3.5 31.8 - - + +
132V ASN* 4.3 0.7 - - - +
133V LEU* 3.1 17.5 + - + -
134V THR* 2.5 50.7 + - - +
136V LYS* 1.3 80.1 + - - +
138V LEU* 1.3 58.4 + - - +
140V ALA* 2.8 26.9 + - - +
141V ILE* 3.0 16.5 + - + +
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Residues in contact with LEU 138 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99V VAL* 4.3 14.8 - - + +
102V MET* 3.7 40.5 - - + +
103V LYS* 3.9 26.9 - - + -
121V LEU* 3.6 31.2 - - + -
130V MET* 4.8 0.2 - - + -
133V LEU* 4.2 28.5 - - + -
134V THR 2.9 14.4 + - - +
135V GLU* 3.9 15.3 - - - +
137V ASP* 1.3 76.9 - - - +
139V VAL* 1.3 60.0 + - - +
141V ILE* 4.2 3.1 - - + -
142V ALA* 3.2 24.6 + - - +
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Residues in contact with VAL 139 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45V ILE* 5.5 7.0 - - + -
47V LEU* 4.4 18.7 - - + +
51V GLN* 4.5 10.1 - - - +
95V ILE* 4.3 17.1 - - + +
99V VAL* 4.7 12.1 - - + -
135V GLU* 2.9 29.6 + - + +
136V LYS* 3.2 11.0 - - - +
137V ASP 2.9 1.2 + - - -
138V LEU* 1.3 77.8 - - - +
140V ALA* 1.3 52.4 + - - +
142V ALA* 3.4 4.5 + - - +
143V GLY* 2.7 32.7 + - - -
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Residues in contact with ALA 140 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47V LEU* 5.3 5.8 - - - -
51V GLN* 4.1 18.4 - - + +
52V TYR* 6.1 0.3 - - - -
54V GLU* 4.5 4.7 - - + -
55V GLY* 3.5 27.8 - - - +
58V LEU* 4.5 5.8 - - + -
136V LYS 3.3 6.3 + - - +
137V ASP* 2.8 14.8 + - - +
139V VAL* 1.3 73.3 - - - +
141V ILE* 1.3 56.2 + - - +
143V GLY* 2.9 3.5 + - - +
144V HIS* 2.7 36.0 + - - +
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Residues in contact with ILE 141 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55V GLY 4.2 8.3 - - - -
58V LEU* 3.4 41.7 - - + +
59V PHE* 4.2 7.1 - - + -
62V ALA* 5.7 0.4 - - + -
63V CYS* 3.7 26.5 - - - -
102V MET* 4.1 8.1 - - - -
133V LEU* 4.2 27.6 - - + -
137V ASP 3.0 16.5 + - - +
138V LEU* 4.1 7.0 - - - +
140V ALA* 1.3 75.0 - - - +
142V ALA* 1.3 62.3 + - - +
144V HIS* 3.3 4.8 + - - +
145V ILE* 3.2 25.2 + - + +
552V HEM 4.0 21.1 - - + -
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Residues in contact with ALA 142 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95V ILE* 4.5 7.0 - - + +
98V LEU* 3.5 29.6 - - + +
99V VAL* 4.3 10.3 - - + -
102V MET* 3.6 18.6 - - + +
138V LEU 3.2 17.7 + - - +
139V VAL 3.5 3.8 - - - +
140V ALA 3.1 0.6 - - - -
141V ILE* 1.3 75.2 - - - +
143V GLY* 1.3 58.6 + - - +
144V HIS 2.9 3.8 - - - -
145V ILE* 2.8 25.2 + - - +
146V LEU* 3.3 8.1 + - - +
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Residues in contact with GLY 143 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47V LEU* 3.8 23.7 - - - +
52V TYR* 6.1 1.1 - - - -
95V ILE* 3.9 13.6 - - - +
139V VAL 2.7 19.6 + - - -
140V ALA 2.9 4.5 + - - -
142V ALA* 1.3 72.7 - - - +
144V HIS* 1.3 58.1 + - - +
146V LEU* 3.5 4.5 + - - +
147V VAL* 3.1 31.2 + - - +
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Residues in contact with HIS 144 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52V TYR* 3.9 17.9 - - + +
55V GLY* 4.1 10.3 - - - -
56V LYS* 3.9 31.5 + - + +
59V PHE* 3.3 46.2 - + + +
140V ALA 2.7 14.4 + - - +
141V ILE 3.3 9.9 - - - +
142V ALA 2.9 0.2 - - - -
143V GLY* 1.3 70.9 - - - +
145V ILE* 1.3 58.0 + - - +
146V LEU 2.9 10.4 + - - -
147V VAL* 3.1 3.7 + - - +
148V GLU* 2.7 68.1 + - + +
156V TRP* 4.7 4.4 - + - -
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Residues in contact with ILE 145 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59V PHE* 3.6 23.1 - - + -
80V LEU* 4.2 27.5 - - + +
82V THR* 4.4 1.2 + - - -
85V LEU* 4.0 24.0 - - + +
98V LEU* 4.0 22.2 - - + -
102V MET* 4.7 1.8 - - + -
141V ILE 3.2 15.3 - - - +
142V ALA* 2.8 13.3 + - - +
144V HIS* 1.3 75.7 - - - +
146V LEU* 1.3 59.7 + - - +
149V PRO* 3.6 17.0 - - - +
156V TRP* 4.0 13.6 + - + -
552V HEM 4.0 31.2 - - + -
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Residues in contact with LEU 146 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36V VAL* 3.8 25.8 - - + +
37V PRO* 4.3 2.5 - - + +
82V THR* 4.5 13.7 + - + +
85V LEU* 4.5 12.1 - - + -
93V ASP* 4.2 19.1 - - - +
94V ASN* 3.9 9.0 - - - -
95V ILE* 3.7 43.3 - - + +
98V LEU* 3.7 17.3 - - + -
142V ALA 3.3 8.5 + - - +
143V GLY 3.9 4.3 - - - +
144V HIS 2.9 1.0 - - - -
145V ILE* 1.3 84.9 - - - +
147V VAL* 1.3 61.1 + - - +
149V PRO* 3.6 12.8 - - - +
150V LYS* 3.7 13.2 - - - +
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Residues in contact with VAL 147 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29V LEU* 4.7 0.4 - - + -
33V VAL* 3.8 22.2 - - + +
34V LEU* 4.5 15.7 - - + -
36V VAL* 3.8 17.7 - - + -
47V LEU* 4.2 12.1 - - + -
52V TYR* 3.9 28.9 - - + -
143V GLY 3.1 17.7 + - - +
144V HIS 3.1 3.0 + - - +
146V LEU* 1.3 79.0 - - - +
148V GLU* 1.3 69.2 + - - +
149V PRO 3.4 0.2 - - - -
150V LYS* 2.7 24.7 + - - +
151V ILE* 3.3 16.0 + - + +
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Residues in contact with GLU 148 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52V TYR* 3.0 22.9 + - - -
56V LYS* 3.9 5.9 + - - -
144V HIS* 2.7 53.7 + - + +
147V VAL* 1.3 75.4 - - - +
149V PRO* 1.3 62.0 - - + +
151V ILE* 2.6 33.8 + - - +
152V LEU* 2.8 41.5 + - - +
156V TRP* 3.6 26.5 - - + -
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Residues in contact with PRO 149 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81V ARG* 5.7 1.3 - - - -
82V THR* 3.4 28.0 - - - +
145V ILE 3.6 11.9 - - - +
146V LEU 3.6 10.3 - - - +
147V VAL 3.5 0.7 - - - -
148V GLU* 1.3 95.5 - - + +
150V LYS* 1.3 58.3 + - + +
151V ILE 3.2 0.2 - - - -
153V GLY* 2.8 31.5 + - - +
156V TRP* 3.5 39.9 - - + -
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Residues in contact with LYS 150 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A LYS* 3.5 13.4 + - - -
32V GLU 4.9 2.9 + - - -
33V VAL* 3.2 37.9 - - + +
35V THR 3.3 26.5 + - - -
36V VAL* 3.7 18.5 - - - +
37V PRO* 5.6 3.0 - - - +
146V LEU 3.7 11.4 - - - +
147V VAL* 2.7 17.5 + - - +
148V GLU 2.7 2.2 + - - -
149V PRO* 1.3 75.3 - - + +
151V ILE* 1.3 60.2 + - - +
153V GLY* 4.8 0.5 + - - -
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Residues in contact with ILE 151 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A LYS* 3.4 42.8 + - + +
311A GLY* 3.4 28.7 - - - +
312A ASN* 3.7 16.5 - - - +
29V LEU* 4.1 5.4 - - + -
33V VAL* 4.3 11.9 - - + -
52V TYR* 3.2 33.9 - - + +
147V VAL* 3.9 21.8 - - + +
148V GLU* 2.6 17.1 + - - +
150V LYS* 1.3 74.8 - - - +
152V LEU* 1.3 64.6 + - + +
153V GLY* 3.7 0.3 + - - -
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Residues in contact with LEU 152 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A HIS* 5.4 2.7 - - + -
307A ILE* 5.6 1.3 - - + -
311A GLY 3.9 13.2 - - - +
312A ASN* 5.2 1.1 - - - +
313A VAL* 3.8 31.0 - - + +
414C ILE* 6.4 1.8 - - + -
69V GLY* 6.3 1.3 - - - -
148V GLU* 2.8 39.2 + - - +
151V ILE* 1.3 78.5 - - + +
153V GLY* 1.3 62.6 + - - +
154V ASP 3.4 2.3 + - - -
155V LYS* 3.5 39.4 + - + +
156V TRP* 4.0 26.5 - - + +
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Residues in contact with GLY 153 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81V ARG* 5.0 2.6 + - - -
149V PRO* 2.8 30.7 + - - +
150V LYS 4.5 0.9 - - - -
151V ILE 3.5 1.6 - - - -
152V LEU* 1.3 70.1 - - - +
154V ASP* 1.3 67.0 - - - +
156V TRP* 3.1 18.4 + - - +
157V GLY 4.1 1.2 + - - -
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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
------------------------------------------------------------
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