Contacts of the helix formed by residues 133 - 149 (chain G) in PDB entry 4DVQ
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 133 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G PRO 5.0 0.2 - - - -
109G CYS* 3.3 31.7 - - - +
110G ARG* 3.3 15.8 + - - +
112G ILE* 3.2 33.3 - - - +
132G LEU* 1.3 73.8 - - - +
134G GLY* 1.3 70.4 + - - +
135G PRO* 3.8 0.9 - - - +
136G GLU* 3.9 7.3 + - - +
137G TRP* 3.6 10.5 + - - -
448G ARG* 2.7 26.8 + - - +
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Residues in contact with GLY 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G HIS* 3.4 35.7 + - - +
108G PRO 5.2 0.6 + - - -
109G CYS* 5.0 2.0 - - - -
133G ASN* 1.3 80.6 - - - +
135G PRO* 1.3 73.9 - - - +
137G TRP* 3.2 15.0 + - - +
138G ARG 3.4 1.9 + - - -
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Residues in contact with PRO 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A LEU* 5.5 13.2 - - + +
478A GLN* 4.4 21.3 - - + +
280E PHE* 5.1 18.8 - - + -
107G HIS* 3.7 26.5 - - + +
133G ASN 4.5 0.2 - - - +
134G GLY* 1.3 80.3 - - - +
136G GLU* 1.3 60.3 + - - +
138G ARG* 3.2 2.2 + - + +
139G PHE* 2.8 31.8 + - - +
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Residues in contact with GLU 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G LYS* 2.8 32.8 + - - +
127G CYS 5.5 0.7 - - - +
132G LEU* 2.9 30.1 - - + +
133G ASN 4.3 6.7 - - - +
134G GLY 3.3 1.0 + - - -
135G PRO* 1.3 80.7 - - - +
137G TRP* 1.3 61.7 + - - +
139G PHE* 3.3 6.3 + - + +
140G ASN* 2.7 41.7 + - - +
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Residues in contact with TRP 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G LEU 3.6 23.1 - - - -
107G HIS* 4.6 6.3 - - - -
108G PRO* 4.1 9.0 - - + -
129G VAL* 3.2 35.1 - - + +
132G LEU* 3.7 30.8 - - - +
133G ASN* 3.6 6.2 + - - -
134G GLY 3.2 13.9 + - - +
136G GLU* 1.3 79.1 - - - +
138G ARG* 1.3 83.5 + - + +
140G ASN* 3.2 3.3 + - - +
141G ARG* 2.7 52.9 + - + +
447G MET* 3.7 39.0 - - + -
448G ARG* 3.4 38.2 - - + +
601G HEM 2.9 19.4 + - - -
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Residues in contact with ARG 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A PRO* 6.2 0.4 - - - -
106G LEU* 3.2 47.5 + - - +
107G HIS* 3.6 28.9 - - + +
134G GLY 3.4 0.8 + - - -
135G PRO 3.2 7.7 + - - +
137G TRP* 1.3 101.3 - - + +
139G PHE* 1.3 69.0 + - - +
141G ARG* 4.2 2.0 - - - -
142G LEU* 3.0 57.8 + - + +
447G MET* 4.5 23.0 - - - +
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Residues in contact with PHE 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278E LEU 5.2 1.1 - - - -
279E ALA 3.7 21.5 - - - +
280E PHE* 3.6 22.7 - + - -
281E ASN* 4.4 0.9 - - - -
282E ARG* 4.0 35.9 - - + -
135G PRO 2.8 21.4 + - - +
136G GLU* 3.7 8.5 - - + +
138G ARG* 1.3 74.9 - - - +
140G ASN* 1.3 65.3 + - - +
142G LEU* 5.9 0.2 - - - -
143G ARG* 2.8 79.9 + - - +
298G GLU 4.4 0.2 - - - -
299G LEU* 3.9 15.5 - - + -
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Residues in contact with ASN 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G CYS 4.7 2.9 - - - +
129G VAL* 3.8 13.5 - - + -
132G LEU* 3.9 16.3 - - + +
136G GLU* 2.7 40.5 + - - +
137G TRP 3.6 6.1 - - - +
139G PHE* 1.3 79.3 - - - +
141G ARG* 1.3 66.4 + - - +
143G ARG* 2.9 14.7 + - - +
144G LEU* 3.1 17.5 + - - +
299G LEU* 4.0 14.8 - - - +
303G ALA* 3.9 16.6 - - - +
307G ASN* 3.2 25.8 + - - +
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Residues in contact with ARG 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G VAL* 3.6 13.1 - - + +
137G TRP* 2.7 44.2 + - + +
138G ARG* 3.9 4.3 - - - +
140G ASN* 1.3 73.1 - - - +
142G LEU* 1.3 59.6 + - + +
144G LEU* 3.1 4.8 + - - +
145G ASN* 3.0 59.6 + - - +
149G LEU* 3.4 20.4 - - - +
447G MET* 3.1 25.9 + - + +
448G ARG 3.6 0.8 - - - -
449G GLN* 2.8 32.1 + - - +
451G LEU* 3.8 16.0 - - - +
601G HEM 2.9 46.3 + - - +
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Residues in contact with LEU 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138G ARG* 3.0 51.0 + - + +
141G ARG* 1.3 76.4 - - + +
143G ARG* 1.3 74.0 + - - +
144G LEU 3.4 0.2 - - - -
145G ASN* 4.5 8.5 - - - +
146G PRO* 3.5 19.7 - - - +
447G MET* 3.9 28.3 - - + -
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Residues in contact with ARG 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280E PHE 4.5 5.5 + - - -
281E ASN* 5.5 5.7 - - - +
282E ARG 5.9 0.4 - - - +
139G PHE* 2.8 78.1 + - - +
140G ASN 2.9 10.2 + - - +
142G LEU* 1.3 95.1 - - - +
144G LEU* 1.3 60.4 + - - +
145G ASN 3.7 0.2 - - - -
146G PRO* 4.1 6.5 - - - +
147G ASP* 5.1 3.1 - - - +
293G LEU* 3.6 18.7 - - - +
296G LYS* 5.6 1.0 + - - +
298G GLU* 3.5 50.2 + - + +
299G LEU* 3.9 16.5 - - + +
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Residues in contact with LEU 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G VAL* 3.9 20.6 - - + -
140G ASN 3.1 17.8 + - - +
141G ARG* 3.1 6.0 + - - +
143G ARG* 1.3 79.7 - - - +
145G ASN* 1.3 65.9 + - - +
146G PRO* 3.2 3.4 - - - -
147G ASP* 3.3 3.5 + - - +
148G VAL* 3.1 30.6 + - + +
293G LEU* 3.9 29.4 - - + -
299G LEU* 4.5 6.5 - - + -
304G ILE* 6.2 0.4 - - - -
307G ASN* 3.2 49.6 - - + +
311G LEU* 5.3 2.7 - - + -
451G LEU* 4.0 26.0 - - + -
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Residues in contact with ASN 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G ARG* 3.0 60.4 + - - +
142G LEU* 4.5 7.3 - - - +
144G LEU* 1.3 76.4 - - - +
146G PRO* 1.3 71.7 - - + +
149G LEU* 3.0 15.8 + - + +
150G SER* 2.9 26.5 + - - +
447G MET* 4.3 17.6 + - - +
451G LEU* 3.4 10.3 - - - +
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Residues in contact with PRO 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142G LEU 3.5 20.0 - - - +
143G ARG* 4.1 6.5 - - - +
144G LEU 3.4 3.6 - - - -
145G ASN* 1.3 96.7 - - + +
147G ASP* 1.3 60.8 + - - +
150G SER* 3.3 24.7 - - - +
152G LYS* 4.9 4.6 - - + +
153G ALA* 3.5 11.3 + - - +
296G LYS* 3.9 21.8 - - - +
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Residues in contact with ASP 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G ARG 5.1 1.6 + - - +
144G LEU 3.3 5.0 + - - +
145G ASN 3.2 0.2 - - - -
146G PRO* 1.3 79.1 - - - +
148G VAL* 1.3 61.5 + - - +
153G ALA* 3.2 19.4 - - - +
156G ARG* 5.4 2.4 + - - -
286G TYR* 4.8 2.1 + - - -
289G ILE* 3.3 28.0 - - + +
292G GLU* 3.6 38.4 - - + +
293G LEU* 4.6 12.7 - - + +
296G LYS* 2.6 40.5 + - - +
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Residues in contact with VAL 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G LEU* 3.1 31.5 + - + +
147G ASP* 1.3 80.6 - - + +
149G LEU* 1.3 60.3 - - - +
150G SER 3.9 0.4 - - - -
153G ALA* 4.5 0.2 - - - -
157G PHE* 3.8 22.7 - - - -
289G ILE* 3.7 29.3 - - + +
293G LEU* 5.1 2.0 - - + -
311G LEU* 4.1 26.9 - - + -
451G LEU* 3.3 35.2 - - + +
452G GLY* 4.6 4.3 - - - -
455G LEU* 4.9 10.8 + - + +
601G HEM 5.6 0.7 - - + -
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Residues in contact with LEU 149 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141G ARG* 3.4 29.2 - - - +
145G ASN* 3.0 23.5 + - + +
148G VAL* 1.3 79.1 - - - +
150G SER* 1.3 58.9 + - - +
154G VAL* 5.0 0.2 - - - -
449G GLN* 4.9 11.4 - - + +
450G CYS 3.7 13.9 - - - +
451G LEU* 3.4 22.2 - - + +
453G ARG* 4.2 10.1 - - + +
454G ARG* 2.7 69.4 + - + +
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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
------------------------------------------------------------
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