Contacts of the helix formed by residues 135 - 149 (chain A) in PDB entry 2BT4
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 VAL 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LEU* 4.4 3.8 - - + -
28A TYR 4.3 13.9 + - - +
29A GLY* 6.0 0.7 - - - -
31A ASP* 3.9 27.6 - - + +
36A VAL* 3.6 29.4 - - + -
39A LEU* 3.7 26.9 - - + +
107A ILE* 4.2 16.8 - - + +
134A GLY* 1.3 66.1 - - - -
136A GLN* 1.3 61.9 + - - +
137A GLY 3.0 5.8 - - - -
138A TYR* 3.0 29.7 + - - +
139A VAL 4.0 1.2 + - - -
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Residues in contact with GLN 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 5.2 1.8 - - - -
133A CYS 3.3 11.0 - - - +
134A GLY* 3.1 0.6 - - - -
135A VAL* 1.3 80.7 - - - +
137A GLY* 1.3 61.8 + - - +
138A TYR 3.2 0.2 - - - -
139A VAL* 3.0 27.2 + - + +
140A PHE* 3.0 42.3 + - + -
743D GLU* 3.5 22.8 + - - +
744D ARG* 3.0 33.0 + - - +
747D ALA* 3.4 16.0 - - - +
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Residues in contact with GLY 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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105A VAL* 3.6 19.1 - - - +
106A HIS 5.8 0.2 - - - -
130A VAL* 3.9 24.8 - - - +
133A CYS* 3.4 7.7 + - - -
134A GLY 3.0 12.6 + - - -
135A VAL 3.0 2.2 - - - -
136A GLN* 1.3 78.7 - - - +
138A TYR* 1.3 56.5 + - - +
140A PHE* 3.3 5.9 + - - +
141A GLY 3.0 22.2 + - - -
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Residues in contact with TYR 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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11A ILE* 4.0 24.2 - - + -
13A ASN* 2.6 30.0 + - - -
17A LEU* 4.1 2.9 - - - +
33A LEU* 4.5 4.0 - - - +
36A VAL* 3.7 32.1 - - + -
39A LEU* 6.0 1.3 - - + -
40A CYS* 3.9 14.6 - - - -
77A VAL* 4.4 12.7 - - + +
79A ASN* 3.1 30.6 + - + +
105A VAL* 4.1 15.9 - - + -
107A ILE* 3.9 28.4 - - + +
135A VAL* 3.0 21.4 + - - +
137A GLY* 1.3 77.4 - - - +
139A VAL* 1.4 58.8 + - + +
141A GLY* 3.2 1.6 + - - -
142A VAL* 2.9 32.8 + - - +
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Residues in contact with VAL 139 (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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39A LEU* 4.2 42.2 - - + +
40A CYS* 6.0 0.2 - - - -
43A ALA* 3.9 20.4 - - + -
135A VAL 4.7 0.2 - - - +
136A GLN* 3.0 25.4 + - + +
138A TYR* 1.4 74.4 - - + +
140A PHE* 1.3 65.5 + - + +
142A VAL* 3.2 2.5 + - - +
143A GLU* 2.8 49.9 + - - +
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Residues in contact with PHE 140 (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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103A VAL* 5.3 0.7 - - - -
130A VAL* 4.1 25.1 - - + -
133A CYS* 3.8 26.7 - - + -
136A GLN* 3.0 50.1 + - + -
137A GLY* 3.3 5.8 + - - +
139A VAL* 1.3 79.9 - - + +
141A GLY* 1.3 63.0 + - - +
143A GLU* 3.2 6.5 + - - -
144A ARG* 3.0 20.4 + - - +
730D VAL* 4.9 0.2 - - + -
740D PHE* 3.3 61.5 - + + -
743D GLU* 3.2 29.2 - - + -
744D ARG* 3.9 7.4 - - + -
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Residues in contact with GLY 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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77A VAL* 3.8 13.7 - - - -
103A VAL* 3.7 30.3 - - - +
137A GLY 3.0 14.5 + - - -
138A TYR 3.2 4.4 + - - -
140A PHE* 1.3 76.3 - - - +
142A VAL* 1.3 56.7 + - - +
144A ARG* 3.3 1.7 + - - +
145A ILE* 2.9 33.1 + - - +
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Residues in contact with VAL 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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4A LEU* 5.7 0.2 - - + -
9A ILE* 4.0 14.9 - - + +
11A ILE* 4.3 23.6 - - + -
40A CYS* 4.6 15.0 - - + +
43A ALA* 3.8 17.0 - - + +
44A ALA* 3.7 32.5 - - - +
47A HIS* 4.8 4.0 - - + -
51A VAL* 5.0 0.9 - - + -
77A VAL* 4.6 1.8 - - + -
138A TYR 2.9 15.1 + - - +
139A VAL 3.2 6.0 + - - +
141A GLY* 1.3 70.9 - - - +
143A GLU* 1.3 68.7 + - - +
145A ILE* 3.3 6.0 + - - +
146A ALA* 2.9 23.0 + - + +
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Residues in contact with GLU 143 (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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43A ALA* 5.4 0.9 - - + -
47A HIS* 3.6 29.5 + - + +
139A VAL* 2.8 41.2 + - + +
140A PHE* 3.2 7.2 + - - +
142A VAL* 1.3 77.1 - - + +
144A ARG* 1.3 54.7 + - - +
146A ALA* 3.5 6.9 + - - +
147A ALA* 3.1 20.3 + - - +
736D GLN* 3.4 15.0 + - - +
740D PHE* 3.3 18.8 - - + -
743D GLU* 2.7 37.4 - - - +
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Residues in contact with ARG 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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103A VAL* 3.7 21.8 - - + -
127A ASP* 6.1 1.7 - - + +
128A GLY* 5.8 1.1 - - - -
140A PHE 3.0 16.9 + - - +
141A GLY* 3.8 4.0 - - - +
143A GLU* 1.3 71.9 - - - +
145A ILE* 1.3 67.7 + - - +
147A ALA* 3.0 9.0 + - - +
148A LEU* 2.9 60.4 + - + +
732D GLY 4.4 5.1 + - - -
733D CYS* 3.1 50.5 + - - +
734D GLY* 3.9 6.3 - - - +
736D GLN* 3.0 30.9 + - - +
740D PHE* 3.9 8.9 - - + -
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Residues in contact with ILE 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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4A LEU* 4.1 9.4 - - + -
9A ILE* 4.0 32.3 - - + -
74A CYS* 4.4 3.6 - - - +
75A GLY* 4.3 11.2 - - - -
76A ILE 4.1 7.4 - - - +
77A VAL* 4.0 15.9 - - + -
101A PRO* 3.7 34.3 - - + +
103A VAL* 4.0 17.5 - - + -
141A GLY 2.9 20.1 + - - +
142A VAL 3.7 4.0 - - - +
144A ARG* 1.3 75.5 - - - +
146A ALA* 1.3 55.0 + - - +
148A LEU* 3.0 3.6 + - + -
149A ALA* 2.7 37.6 + - + +
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Residues in contact with ALA 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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4A LEU* 3.7 32.6 - - + +
47A HIS* 3.8 26.9 - - + +
142A VAL* 2.9 18.1 + - + +
143A GLU 3.7 5.6 - - - +
144A ARG 3.2 0.2 - - - -
145A ILE* 1.3 77.6 - - - +
147A ALA* 1.3 61.5 + - - +
149A ALA 3.8 1.6 + - - -
150A GLY* 3.7 13.7 + - - -
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Residues in contact with ALA 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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143A GLU 3.1 9.2 + - - +
144A ARG* 3.0 12.1 + - - +
146A ALA* 1.3 76.2 - - - +
148A LEU* 1.3 64.8 + - + +
150A GLY 3.3 18.2 + - - +
736D GLN* 3.4 31.0 - - - +
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Residues in contact with LEU 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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101A PRO* 4.0 28.4 - - + +
103A VAL* 5.6 0.9 - - + -
127A ASP* 5.0 14.8 - - + -
144A ARG* 2.9 62.5 + - + +
145A ILE* 3.8 2.9 - - + +
147A ALA* 1.3 74.8 - - - +
149A ALA* 1.3 59.8 + - - +
150A GLY 2.9 14.4 + - - +
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Residues in contact with ALA 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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2A ARG 4.0 17.7 - - - +
3A SER* 3.8 19.9 - - - -
4A LEU* 3.8 22.9 + - + +
74A CYS* 4.2 15.9 - - + +
101A PRO* 4.7 4.3 - - + -
145A ILE* 2.7 22.4 + - + +
146A ALA 4.1 3.6 - - - -
147A ALA 3.4 0.2 - - - -
148A LEU* 1.3 71.9 - - - +
150A GLY* 1.3 54.7 + - - +
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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