Contacts of the helix formed by residues 129 - 140 (chain B) in PDB entry 4LQL
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 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B MET* 4.4 9.8 - - - +
82B THR 4.8 0.9 - - - -
83B PHE* 4.0 28.5 - - - -
84B SER 5.1 4.0 + - - +
125B GLN 3.7 5.9 + - - -
126B SER 3.3 1.2 + - - -
127B ALA 3.7 0.2 - - - -
128B HIS* 1.3 78.3 - - - +
130B ASP* 1.3 72.7 + - - +
131B ARG 3.0 1.3 - - - +
132B GLU* 3.0 12.4 + - - +
133B TYR* 3.0 11.3 + - - +
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Residues in contact with ASP 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A MET* 5.6 4.9 - - + -
79B TRP* 5.0 2.7 - - + -
80B MET* 4.2 13.4 + - + +
102B HIS* 4.8 9.8 - - + -
103B LEU 4.9 12.8 - - - +
104B ALA* 5.1 11.2 - - + -
126B SER* 3.0 27.2 + - - +
129B GLY* 1.3 73.5 - - - +
131B ARG* 1.3 57.8 + - + +
133B TYR* 2.8 27.2 + - - +
134B ALA* 3.1 12.3 + - - +
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Residues in contact with ARG 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332A ASP* 3.5 27.5 + - - +
344A ILE* 5.0 9.3 - - - +
426A TRP* 5.6 3.0 - - - -
432A LEU* 4.9 7.7 - - - +
436A ALA* 3.8 31.3 - - - +
439A TRP* 3.9 39.0 - - + +
440A MET* 4.5 16.6 - - + +
443A GLY 5.5 1.0 - - - +
444A GLY 5.4 0.3 - - - +
445A GLY* 4.0 36.6 + - - -
446A HIS* 4.7 3.6 - - - +
126B SER 4.1 1.0 + - - -
127B ALA 3.7 20.7 + - - +
128B HIS* 4.6 6.3 - - - -
129B GLY 3.0 1.0 - - - +
130B ASP* 1.3 79.6 - - + +
132B GLU* 1.3 59.1 + - - +
134B ALA* 3.4 19.9 - - - +
135B TYR* 3.6 6.4 + - - +
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A VAL* 3.2 14.0 - - - +
189A ALA* 2.9 32.6 + - - +
190A VAL* 3.6 24.1 + - + +
446A HIS* 3.7 22.8 + - + +
83B PHE* 4.2 13.6 - - + -
84B SER 3.6 4.9 - - - +
85B PRO* 3.2 9.0 - - - +
86B ALA* 2.6 40.4 + - - +
128B HIS 4.3 2.1 + - - +
129B GLY* 3.0 10.8 + - - +
131B ARG* 1.3 74.9 - - - +
133B TYR* 1.3 65.2 + - - +
135B TYR* 3.9 6.7 + - - +
136B ILE 4.1 1.4 + - - -
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Residues in contact with TYR 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B THR* 5.1 5.4 - - - -
80B MET* 4.2 22.2 - - + -
84B SER* 5.3 4.0 + - - +
86B ALA* 5.2 1.8 - - - -
89B TRP* 5.1 18.2 - + - +
102B HIS* 3.7 25.6 - + + -
129B GLY 3.0 9.1 + - - +
130B ASP 2.8 15.9 + - - +
132B GLU* 1.3 70.4 - - - +
134B ALA* 1.3 56.3 + - - +
136B ILE* 2.7 44.3 + - + +
137B ASN* 3.4 8.6 + - + +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A TRP 5.3 0.4 - - - +
440A MET* 3.2 45.3 - - + +
443A GLY 5.8 1.1 - - - +
102B HIS* 5.1 6.0 - - + -
130B ASP 3.1 6.6 + - - +
131B ARG* 3.4 13.9 - - - +
133B TYR* 1.3 81.1 - - - +
135B TYR* 1.3 51.4 + - - +
137B ASN* 3.2 6.3 + - - +
138B SER* 2.6 37.1 + - - -
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Residues in contact with TYR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ALA* 5.3 2.5 - - + -
190A VAL* 3.9 36.6 - - + -
394A SER* 5.5 3.4 - - - -
396A PHE* 6.2 3.1 - + - -
443A GLY* 4.6 6.0 - - - -
444A GLY* 4.3 20.2 - - - +
445A GLY 5.2 0.2 - - - +
131B ARG 3.6 7.1 + - - +
132B GLU 4.3 4.0 - - - +
133B TYR 2.8 3.6 + - - -
134B ALA* 1.3 77.1 - - - +
136B ILE* 1.3 63.5 + - + +
138B SER* 4.1 6.1 - - - -
139B ARG* 2.8 35.6 + - + +
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Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ALA* 4.0 7.2 - - + -
86B ALA* 3.5 30.5 - - + +
89B TRP* 4.2 21.1 - - + +
90B ILE* 3.6 24.5 - - + -
93B THR* 4.7 9.7 - - - +
132B GLU 4.1 0.6 + - - -
133B TYR* 2.7 19.4 + - + +
135B TYR* 1.3 84.8 - - + +
137B ASN* 1.3 61.9 + - + +
139B ARG* 4.3 8.1 - - + -
140B LEU* 3.1 31.8 - - + +
142B VAL* 4.8 0.2 - - - +
196E VAL* 3.4 32.8 - - + -
200E ILE* 5.0 3.4 - - + -
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B THR* 5.4 4.0 - - - +
100B LEU* 5.0 12.6 - - + -
133B TYR* 3.4 11.6 + - + +
134B ALA* 3.2 9.0 + - - +
135B TYR 3.1 0.4 - - - -
136B ILE* 1.3 85.8 - - + +
138B SER* 1.3 56.9 + - - +
141B ASN* 3.9 1.1 - - - -
142B VAL* 3.0 53.6 + - + +
144B ALA* 5.3 5.2 - - + +
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Residues in contact with SER 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A MET 4.4 2.7 - - - -
441A LYS* 3.2 30.7 - - - -
443A GLY* 4.2 10.3 - - - -
134B ALA 2.6 21.0 + - - -
135B TYR* 3.9 6.7 - - - -
137B ASN* 1.3 74.0 - - - +
139B ARG* 1.3 69.9 + - - +
141B ASN* 3.0 17.0 + - - +
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Residues in contact with ARG 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A TYR 3.1 14.2 + - - -
396A PHE* 3.6 30.4 - - - +
397A ASP* 3.0 36.5 - - - +
135B TYR* 2.8 28.7 + - + +
136B ILE* 4.3 10.5 - - + +
138B SER* 1.3 76.4 - - - +
140B LEU* 1.3 61.0 + - - +
141B ASN* 2.9 14.9 + - - -
194E ASP* 3.7 18.8 + - - -
196E VAL* 3.9 13.8 - - + +
197E ALA* 3.7 33.7 - - - +
200E ILE* 4.1 20.8 - - + +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ILE* 5.3 3.6 - - + +
93B THR* 5.4 7.9 - - - +
94B GLU* 5.3 13.0 - - + -
136B ILE* 3.1 27.8 + - + +
138B SER 3.3 0.6 - - - -
139B ARG* 1.3 78.4 - - - +
141B ASN* 1.3 67.1 + - - +
142B VAL* 4.1 14.9 - - + +
200E ILE* 3.7 35.9 - - + -
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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