Contacts of the helix formed by residues 129 - 146 (chain A) in PDB entry 4LZ6
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 129 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLY 2.8 5.7 + - - -
128A ALA* 1.3 71.2 - - - +
130A SER* 1.3 60.9 + - - +
131A VAL* 3.1 19.3 - - + -
132A THR* 2.8 24.0 + - - +
133A GLN* 2.6 32.0 + - - -
267A LEU* 3.1 29.1 - - - +
271A SER* 4.0 11.9 + - - -
272A ASP* 4.3 11.0 - - - +
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Residues in contact with SER 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ALA 3.7 4.2 + - - -
129A THR* 1.3 72.6 - - - +
131A VAL* 1.3 63.6 + - - +
133A GLN* 3.4 17.5 - - - +
134A GLY* 3.5 4.0 + - - -
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLU* 4.2 25.1 - - + -
129A THR* 2.9 22.6 + - + -
130A SER* 1.3 77.2 - - - +
132A THR* 1.3 68.8 + - - +
134A GLY* 3.0 9.5 + - - -
135A TYR* 3.0 32.3 + - + +
272A ASP* 5.0 4.3 - - - +
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Residues in contact with THR 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLU 2.6 26.6 + - - -
54A ALA* 3.5 4.0 - - + +
55A GLY 3.0 18.9 + - - -
58A ILE* 3.3 20.8 - - + +
127A GLY 4.6 2.2 - - - +
128A ALA* 5.1 0.9 - - - -
129A THR* 2.8 40.4 + - - +
131A VAL* 1.3 75.2 - - - +
133A GLN* 1.3 68.7 + - - +
135A TYR* 3.0 4.2 + - - -
136A ALA* 2.8 27.4 + - - +
267A LEU* 5.4 2.2 - - + -
272A ASP* 4.0 10.3 - - - +
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Residues in contact with GLN 133 (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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58A ILE* 5.5 1.1 - - - -
120A GLY* 4.7 5.7 + - - -
123A LEU* 3.3 19.8 - - - +
124A GLN* 3.3 36.9 + - - +
128A ALA* 2.7 37.1 - - + +
129A THR 2.6 22.4 + - - +
130A SER* 3.4 12.1 - - - +
132A THR* 1.3 76.9 - - - +
134A GLY* 1.3 65.6 + - - +
136A ALA* 5.2 0.2 - - - -
137A THR* 2.9 28.5 + - - +
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Residues in contact with GLY 134 (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 SER 3.5 4.6 + - - -
131A VAL 3.0 8.5 + - - -
133A GLN* 1.3 80.9 - - - +
135A TYR* 1.3 57.6 + - - +
137A THR* 3.4 7.8 + - - -
138A ASP* 2.8 42.2 + - - +
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Residues in contact with TYR 135 (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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48A VAL* 3.5 26.8 - - + +
51A GLU* 3.2 25.3 + - + +
52A GLY* 4.1 15.5 - - - -
55A GLY* 4.3 3.4 - - - -
131A VAL* 3.0 45.8 + - + +
132A THR* 3.0 9.7 + - - +
134A GLY* 1.3 76.6 - - - +
136A ALA* 1.3 57.8 + - - +
138A ASP* 3.0 13.4 + - - +
139A TYR* 2.9 23.4 + - - -
195A VAL* 3.5 27.9 - - + +
196A LEU* 5.3 11.7 - - + -
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Residues in contact with ALA 136 (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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55A GLY* 3.2 33.5 - - - +
58A ILE* 4.2 6.1 - - + -
59A ALA* 3.9 6.7 - - + +
123A LEU* 3.9 24.8 - - + +
132A THR 2.8 17.0 + - - +
135A TYR* 1.3 69.8 - - - +
137A THR* 1.3 59.1 + - - +
139A TYR* 3.4 6.0 - - - +
140A LEU* 2.8 33.8 + - - +
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Residues in contact with THR 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 4.2 18.6 - - + +
120A GLY* 5.2 4.6 - - - +
123A LEU* 3.2 16.0 - - - +
133A GLN* 2.9 25.7 + - - +
134A GLY* 3.5 12.2 - - - -
136A ALA* 1.3 72.9 - - - +
138A ASP* 1.3 64.3 + - - +
139A TYR 3.1 0.2 + - - -
140A LEU 3.2 0.7 + - - -
141A PHE* 2.9 46.3 + - + +
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Residues in contact with ASP 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLY* 2.8 28.7 + - - +
135A TYR* 3.3 13.2 + - + +
137A THR* 1.3 82.4 - - - +
139A TYR* 1.3 56.5 + - - +
141A PHE* 5.1 1.6 - - - -
142A PRO* 3.3 18.4 - - - +
195A VAL* 4.1 2.5 - - + -
196A LEU* 3.3 49.5 - - + +
199A SER* 3.4 9.0 + - - -
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Residues in contact with TYR 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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36A TYR* 5.1 7.6 + - - -
44A ILE* 6.0 2.5 - - + -
56A VAL* 4.2 30.8 - - + +
59A ALA* 3.4 27.4 - - + -
60A PHE* 5.2 6.2 - + - -
63A MET* 5.7 8.4 - - + -
135A TYR 2.9 11.7 + - - +
136A ALA* 3.4 11.0 - - - +
137A THR 3.0 0.2 - - - -
138A ASP* 1.3 77.6 - - - +
140A LEU* 1.3 64.5 + - + +
141A PHE 3.4 0.2 - - - -
142A PRO* 3.3 9.5 - - - +
143A ILE* 3.1 48.3 - - + +
195A VAL* 3.6 19.7 - - + +
198A ALA* 5.2 5.8 - - + -
199A SER* 3.4 19.1 - - - -
202A THR* 6.0 5.1 - - - +
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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
----------------------------------------------------------
59A ALA* 3.2 38.1 - - + +
62A ILE* 3.8 33.9 - - + -
63A MET* 4.9 9.0 - - + +
119A LEU* 3.9 22.0 - - + +
123A LEU* 3.8 21.3 - - + -
136A ALA 2.8 16.2 + - - +
139A TYR* 1.3 81.8 - - + +
141A PHE* 1.3 67.5 + - - +
143A ILE* 3.4 8.9 + - + +
144A LEU* 3.0 38.0 + - + +
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Residues in contact with PHE 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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115A ALA* 4.1 27.8 - - + -
116A PHE* 4.3 17.7 - + + -
119A LEU* 3.9 23.0 - - + +
137A THR* 2.9 32.0 + - + +
138A ASP* 5.0 1.8 - - - +
140A LEU* 1.3 73.4 - - - +
142A PRO* 1.4 74.5 - - + +
144A LEU* 3.1 9.9 + - - +
145A LEU* 3.3 37.7 + - + +
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Residues in contact with PRO 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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138A ASP* 3.3 15.5 - - - +
139A TYR 3.3 1.8 - - - +
141A PHE* 1.4 92.9 - - + +
143A ILE* 1.3 53.9 + - - +
144A LEU 2.6 1.4 + - - -
145A LEU* 2.5 50.4 + - + +
146A GLY* 3.4 4.3 - - - -
196A LEU 4.6 0.9 - - - +
199A SER* 2.7 43.7 - - - +
200A ILE* 4.1 22.7 - - + +
203A VAL* 4.2 5.1 - - + +
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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
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63A MET* 4.7 15.9 - - + -
66A MET* 5.1 7.4 - - - +
139A TYR* 3.1 61.0 - - + +
140A LEU* 3.8 13.0 - - + +
141A PHE 3.3 1.0 - - - -
142A PRO* 1.3 74.1 - - - +
144A LEU* 1.3 61.4 + - + +
146A GLY* 3.1 5.2 - - - +
147A SER* 3.0 19.1 + - - -
150A PHE* 4.1 36.1 - - + -
199A SER* 4.1 13.5 - - - +
202A THR* 5.8 4.9 - - + -
203A VAL* 4.2 11.0 - - + +
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Residues in contact with LEU 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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62A ILE* 5.7 5.4 - - + -
66A MET* 6.1 9.0 - - + -
111A GLY* 3.0 26.9 - - - +
112A PHE* 4.0 8.7 - - - +
114A SER* 3.2 19.3 - - - +
115A ALA* 3.4 24.7 - - + +
119A LEU* 4.4 7.0 - - + -
140A LEU* 3.0 43.4 + - + +
141A PHE 3.1 3.3 + - - +
142A PRO 2.6 5.7 + - - -
143A ILE* 1.3 77.7 - - + +
145A LEU* 1.3 56.7 + - - +
147A SER* 2.3 41.6 + - - +
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Residues in contact with LEU 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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112A PHE* 2.8 44.6 - - + +
115A ALA* 4.2 9.9 - - + -
141A PHE* 3.3 43.3 - - + +
142A PRO* 2.5 31.7 + - + +
144A LEU* 1.3 71.5 - - - +
146A GLY* 1.3 45.5 + - - +
147A SER 3.6 0.2 - - - -
148A ILE* 4.9 4.3 - - - +
149A PHE* 5.4 0.4 - - - -
203A VAL* 6.1 0.9 - - + -
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Residues in contact with GLY 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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142A PRO 3.4 9.6 - - - -
143A ILE 3.1 9.4 - - - +
144A LEU 3.3 0.4 - - - -
145A LEU* 1.3 74.5 + - - +
147A SER* 1.3 65.3 + - - +
148A ILE* 3.0 5.8 + - - +
149A PHE* 3.5 29.7 + - - +
150A PHE* 3.8 6.9 + - - +
203A VAL* 3.9 20.3 - - - +
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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