Contacts of the helix formed by residues 134 - 150 (chain A) in PDB entry 4B7B
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 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A GLN* 3.6 11.0 - - - -
114A THR 3.5 11.4 - - - -
115A MET 3.7 0.9 - - - -
116A GLU 2.8 25.3 + - - -
132A LEU 3.5 0.8 + - - -
133A ASP* 1.3 75.6 - - - +
135A ILE* 1.3 66.6 + - - -
136A ILE 3.4 2.6 + - - -
137A PRO* 3.5 2.5 - - - +
138A ARG* 3.3 25.6 + - - +
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 4.5 9.6 - - + -
82A TYR* 4.2 9.9 - - + -
86A VAL* 3.8 30.3 - - + -
101A ILE* 4.6 3.4 - - + -
114A THR* 2.9 28.7 + - + +
115A MET* 3.1 19.1 + - + +
134A GLY* 1.3 71.0 - - - -
136A ILE* 1.3 59.2 + - - +
138A ARG* 3.3 2.3 + - - +
139A THR* 2.8 45.1 + - - +
263A LEU* 3.9 26.7 - - + -
333A ILE* 3.6 31.0 - - + -
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Residues in contact with ILE 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A MET* 2.8 28.2 + - + +
116A GLU* 4.3 17.0 - - + -
135A ILE* 1.3 71.6 - - - +
137A PRO* 1.3 71.4 - - + +
139A THR* 3.3 1.8 + - - -
140A LEU* 3.2 29.0 + - + +
210A VAL* 3.8 13.0 - - + -
214A LEU* 4.3 10.8 - - + -
239A PHE* 3.7 57.2 - - + -
263A LEU* 3.7 34.5 - - + +
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Residues in contact with PRO 137 (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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115A MET 4.2 0.9 - - - +
116A GLU* 3.6 25.1 - - - +
133A ASP* 3.8 22.9 - - - +
134A GLY 3.5 7.4 - - - +
136A ILE* 1.3 97.6 - - + +
138A ARG* 1.3 58.5 + - - +
140A LEU* 3.6 0.9 + - - +
141A HIS* 2.5 34.6 + - - -
210A VAL* 4.3 14.8 - - + -
211A TYR* 3.7 30.3 - - + +
214A LEU* 4.4 8.7 - - + -
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Residues in contact with ARG 138 (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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78A GLN* 3.3 12.5 + - - +
79A ILE* 3.4 34.0 - - - +
82A TYR* 3.7 40.5 + - + -
130A VAL* 3.0 35.5 + - - +
131A PRO* 3.2 19.6 + - - +
133A ASP* 3.0 31.3 + - + +
134A GLY 3.3 14.9 + - - +
135A ILE 3.3 1.2 + - - -
136A ILE 3.3 0.6 - - - -
137A PRO* 1.3 78.2 - - - +
139A THR* 1.3 58.0 + - - +
141A HIS* 3.3 8.3 + - - +
142A GLN* 3.0 29.5 + - - +
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Residues in contact with THR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 3.7 8.0 - - - -
86A VAL* 3.7 20.5 - - + +
90A LEU* 4.0 10.5 - - + +
135A ILE* 2.8 29.4 + - - +
136A ILE* 3.7 7.0 - - - -
137A PRO 3.2 0.2 - - - -
138A ARG* 1.3 74.9 - - - +
140A LEU* 1.3 63.9 + - + +
142A GLN* 3.4 0.9 + - - -
143A ILE* 2.9 54.2 + - + +
241A VAL* 5.2 2.5 - - + -
261A LEU* 3.7 24.0 - - + +
263A LEU* 4.2 7.0 - - + +
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ILE* 3.2 18.0 + - + +
137A PRO 4.1 0.7 - - - +
138A ARG 3.4 0.2 - - - -
139A THR* 1.3 79.6 - - + +
141A HIS* 1.3 60.5 + - - +
143A ILE* 3.8 5.9 - - + +
144A PHE* 3.1 38.1 + - + -
156A VAL* 3.9 28.3 - - + -
158A VAL* 4.6 1.6 - - + -
204A VAL* 4.0 22.2 - - + -
207A LYS* 4.5 3.8 - - - +
210A VAL* 3.7 41.1 - - + -
239A PHE* 4.3 17.9 - - + -
241A VAL* 4.3 15.3 - - + -
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Residues in contact with HIS 141 (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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130A VAL* 5.9 2.2 - - + +
133A ASP* 4.9 1.3 - - - -
137A PRO 2.5 22.6 + - - +
138A ARG* 3.4 11.7 - - - +
139A THR 3.2 0.4 - - - -
140A LEU* 1.3 76.3 - - - +
142A GLN* 1.3 60.7 + - - +
144A PHE* 3.3 4.0 + - - +
145A GLU* 2.9 29.5 + - - +
207A LYS* 3.3 52.0 + - + +
208A ASP* 3.4 3.0 + - - -
210A VAL* 4.7 1.1 - - + -
211A TYR* 3.4 26.6 + + - -
1370A CD 2.6 28.8 - - - -
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Residues in contact with GLN 142 (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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82A TYR* 2.6 45.4 + - + +
87A CYS* 3.5 23.7 - - - -
90A LEU* 3.5 15.6 - - + +
138A ARG 3.0 10.9 + - - +
141A HIS* 1.3 75.6 - - - +
143A ILE* 1.3 65.2 + - - +
145A GLU* 4.3 7.9 - - + -
146A LYS* 2.8 62.7 + - + +
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 3.6 22.7 - - + -
94A ILE* 5.1 3.6 - - + -
139A THR* 2.9 42.8 + - + +
140A LEU* 3.8 10.5 - - + +
141A HIS 3.2 0.2 - - - -
142A GLN* 1.3 78.0 - - - +
144A PHE* 1.3 65.6 + - + +
146A LYS* 5.1 1.3 - - - -
147A LEU* 3.2 38.7 + - + +
154A PHE* 4.7 0.7 - - + -
156A VAL* 4.2 20.9 - - + -
241A VAL* 4.0 20.2 - - + -
243A ILE* 3.8 31.2 - - + -
261A LEU* 5.7 0.4 - - + -
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Residues in contact with PHE 144 (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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140A LEU* 3.1 32.5 + - + +
141A HIS 3.8 0.2 - - - +
143A ILE* 1.3 79.2 - - + +
145A GLU* 1.3 58.2 + - - +
148A THR* 2.7 34.7 + - - -
154A PHE* 3.7 26.0 - + - -
156A VAL* 4.1 20.0 - - + -
204A VAL* 3.3 42.6 - - + -
205A HIS 3.5 17.5 - - - -
206A ASN* 3.6 17.3 - - - -
207A LYS* 3.7 28.3 - - + -
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Residues in contact with GLU 145 (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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141A HIS 2.9 21.3 + - - +
142A GLN* 3.8 9.6 - - + +
144A PHE* 1.3 70.1 - - - +
146A LYS* 1.3 62.9 + - + +
148A THR* 4.0 1.6 - - - -
149A ASP* 3.1 36.6 + - - +
207A LYS* 3.2 16.7 + - - +
1369A CD 2.3 27.0 - - - -
1377A CL 3.5 11.7 - - - +
1385A CO 2.6 24.1 + - - -
1386A CO 2.7 15.0 + - - +
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Residues in contact with LYS 146 (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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87A CYS* 4.8 0.2 - - - -
90A LEU* 5.6 1.7 - - + +
91A ASP* 3.2 21.4 + - - +
94A ILE* 4.0 27.8 - - + +
142A GLN* 2.8 53.1 + - + +
143A ILE 4.3 0.2 - - - +
145A GLU* 1.3 76.3 - - + +
147A LEU* 1.3 62.4 + - + +
149A ASP* 3.6 5.3 + - - +
150A ASN* 3.3 29.4 + - - +
1368A CD 4.1 0.4 - - - -
1383A CO 3.1 24.5 + - - -
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Residues in contact with LEU 147 (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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94A ILE* 4.1 32.5 - - + -
143A ILE* 3.2 25.2 + - + +
146A LYS* 1.3 79.0 - - + +
148A THR* 1.3 62.5 + - - +
150A ASN* 2.8 23.7 - - - +
152A THR* 3.0 35.3 + - + +
154A PHE* 3.4 32.8 - - + -
243A ILE* 3.7 30.3 - - + -
245A MET* 3.7 16.2 - - + -
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Residues in contact with THR 148 (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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144A PHE* 2.7 26.4 + - - +
145A GLU* 4.0 3.6 - - - -
147A LEU* 1.3 79.2 - - - +
149A ASP* 1.3 65.7 + - - +
151A GLY* 3.3 11.9 + - - -
152A THR 5.1 1.6 - - - -
154A PHE* 3.8 15.4 - - - -
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Residues in contact with ASP 149 (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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145A GLU* 3.1 22.8 + - - +
146A LYS* 3.9 6.0 - - - +
147A LEU 3.4 0.2 - - - -
148A THR* 1.3 83.3 - - - +
150A ASN* 1.3 58.1 + - + +
151A GLY 3.2 2.3 + - - -
1369A CD 2.8 17.1 - - - -
1386A CO 2.1 30.5 + - - -
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Residues in contact with ASN 150 (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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94A ILE* 5.6 3.4 - - - +
146A LYS* 3.3 15.1 + - - +
147A LEU* 2.8 22.8 - - - +
149A ASP* 1.3 76.8 - - + +
151A GLY* 1.3 59.5 + - - +
152A THR* 2.6 29.9 + - - -
247A GLU* 5.0 13.5 + - - +
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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
------------------------------------------------------------
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