Contacts of the helix formed by residues 107 - 120 (chain D) in PDB entry 3LOC
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 TYR 107 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D LEU* 6.0 4.5 - - + -
72D ILE* 6.2 0.4 - - + -
75D ILE* 4.6 32.6 - - + +
103D VAL* 2.8 44.1 + - + +
106D ASP* 1.3 94.4 - - + +
108D PRO* 1.3 63.6 - - - +
109D GLN 3.4 2.2 - - - -
110D ALA* 3.2 16.4 + - + +
111D SER* 3.2 19.6 + - - -
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Residues in contact with PRO 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D SER 3.6 15.2 - - - +
105D ARG 3.7 12.6 - - - +
106D ASP 3.2 10.5 - - - +
107D TYR* 1.3 88.8 - - - +
109D GLN* 1.3 69.4 + - + +
111D SER* 3.6 1.6 - - - -
112D ARG* 3.0 44.3 + - - +
173D ALA* 4.0 18.2 - - + +
188D ARG* 5.6 7.0 - - - +
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Residues in contact with GLN 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D LEU* 3.9 16.1 - - + +
28D ASP* 3.3 31.3 + - - +
31D SER* 3.4 28.2 + - - +
32D GLN* 5.2 4.7 - - - +
107D TYR 3.4 1.2 - - - -
108D PRO* 1.3 82.9 - - + +
110D ALA* 1.3 57.4 + - - +
112D ARG* 3.5 25.1 + - - +
113D LEU* 3.0 27.2 + - - +
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D LEU* 3.9 21.3 - - + +
72D ILE* 3.2 45.2 - - + +
75D ILE* 6.6 0.2 - - + -
107D TYR* 3.2 23.1 + - + +
108D PRO 3.2 0.2 - - - -
109D GLN* 1.3 75.7 - - - +
111D SER* 1.3 67.4 + - - +
113D LEU* 3.2 1.2 + - - +
114D PHE* 3.0 19.6 + - - +
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Residues in contact with SER 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C PHE* 5.8 0.2 - - - -
72D ILE* 4.6 0.8 - - - +
76D TRP* 3.7 29.1 - - - -
103D VAL* 6.3 0.7 - - - -
104D SER* 5.1 4.5 + - - -
107D TYR 3.2 9.8 + - - -
108D PRO 3.6 7.2 - - - -
110D ALA* 1.3 81.3 - - - +
112D ARG* 1.3 56.5 + - - +
114D PHE* 3.2 3.5 + - - +
115D CYS* 2.9 29.6 + - - +
170D GLN* 4.0 9.2 - - - +
173D ALA* 4.0 14.1 - - - +
174D ASP* 2.7 25.8 + - - +
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Residues in contact with ARG 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C MSE 5.3 1.3 - - - -
119C LEU* 3.7 45.5 + - + +
31D SER* 5.2 9.8 + - - -
32D GLN* 5.2 7.9 + - - -
108D PRO* 3.0 42.4 + - - +
109D GLN* 3.7 25.7 + - - +
111D SER* 1.3 73.7 - - - +
113D LEU* 1.3 58.6 + - - +
115D CYS* 3.3 5.7 + - - +
116D MSE 2.9 29.5 + - - +
173D ALA 4.4 12.8 + - - +
174D ASP* 4.1 16.4 - - - +
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Residues in contact with LEU 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D LEU* 4.1 10.1 - - + -
30D PHE* 3.9 24.0 - - + +
31D SER* 3.9 27.8 - - - +
34D GLY* 5.8 1.6 - - - -
35D PHE 6.1 0.2 - - - +
65D TYR* 4.3 18.0 + - + +
68D VAL* 3.8 28.9 - - + -
69D LEU* 4.0 14.4 - - + -
72D ILE* 4.8 0.7 - - + -
109D GLN 3.0 18.4 + - - +
110D ALA 3.2 6.0 + - - +
112D ARG* 1.3 75.9 - - - +
114D PHE* 1.3 63.3 + - - +
116D MSE 3.3 11.2 + - + +
117D GLU* 3.1 22.0 + - - +
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Residues in contact with PHE 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C PHE* 4.0 5.4 - + - -
178C GLN* 3.4 30.1 - - - -
69D LEU* 3.7 21.0 - - + +
72D ILE* 4.6 3.1 - - + -
73D LEU* 3.6 32.1 - - + -
76D TRP* 3.3 33.7 - + + -
110D ALA 3.0 11.4 + - - +
111D SER 3.5 2.9 - - - +
113D LEU* 1.3 75.5 - - - +
115D CYS* 1.3 65.8 + - - +
117D GLU* 3.2 6.3 + - - +
118D MSE 3.1 39.6 + - + +
125D LEU* 3.6 30.5 - - + -
129D LEU* 4.4 3.1 - - + -
212D URA 3.7 10.5 - - - -
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Residues in contact with CYS 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C CYS* 3.7 29.2 - - - -
119C LEU* 3.9 13.9 - - + -
175C PHE* 3.9 26.7 - - + -
111D SER 2.9 17.1 + - - +
112D ARG 3.4 5.8 - - - +
114D PHE* 1.3 78.0 - - - +
116D MSE 1.3 64.1 + - - +
118D MSE 2.8 6.0 + - - +
119D LEU* 2.8 26.4 + - - +
174D ASP* 3.5 24.2 - - - +
175D PHE* 5.8 0.4 - - - -
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Residues in contact with MSE 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C MSE 3.7 35.2 - - + +
119C LEU* 3.6 31.5 - - + +
120C ALA* 5.4 2.9 - - + +
65D TYR* 5.8 0.9 - - - +
112D ARG 2.9 19.4 + - - +
113D LEU* 3.7 13.5 - - + +
115D CYS* 1.3 72.5 - - - +
117D GLU* 1.3 61.5 + - - +
119D LEU* 3.3 11.0 + - - +
120D ALA* 3.1 23.8 + - + +
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Residues in contact with GLU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D TYR* 2.6 45.0 + - - +
69D LEU* 3.8 18.2 - - + -
113D LEU 3.1 9.5 + - - +
114D PHE 3.5 8.7 - - - +
115D CYS 3.1 0.4 - - - -
116D MSE 1.3 74.9 - - - +
118D MSE 1.3 63.7 + - - +
120D ALA* 3.4 6.7 + - - +
121D GLY 3.4 4.2 + - - -
122D ALA* 2.9 36.2 + - + -
123D PRO* 3.1 11.2 - - - +
124D LEU* 2.8 30.0 + - - +
125D LEU* 3.1 24.2 + - + -
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Residues in contact with MSE 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C ARG* 5.6 0.7 - - - -
174C ASP 3.6 16.5 - - - +
175C PHE* 3.6 29.8 - - + +
177C PRO* 3.2 37.6 - - + +
178C GLN* 3.1 38.8 - - + +
114D PHE* 3.1 33.2 + - + +
115D CYS* 2.8 9.0 + - - +
117D GLU* 1.3 76.3 - - - +
119D LEU* 1.3 56.5 + - - +
121D GLY* 2.7 26.9 + - - -
122D ALA* 4.3 5.2 - - + +
125D LEU* 5.5 0.9 - - - -
129D LEU* 3.8 20.0 - - + -
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Residues in contact with LEU 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C ARG* 3.6 43.2 + - + +
115C CYS* 3.7 25.6 - - + -
116C MSE 3.5 56.2 - - + +
119C LEU* 3.9 18.2 - - + -
174C ASP* 3.8 18.4 - - + +
115D CYS* 2.8 22.8 + - - +
116D MSE 3.3 10.7 + - - +
118D MSE 1.3 73.2 - - - +
120D ALA* 1.3 59.3 + - - +
121D GLY 3.4 0.5 + - - -
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Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D MSE 3.1 16.4 + - + +
117D GLU* 3.8 8.3 - - - +
118D MSE 3.1 1.0 - - - -
119D LEU* 1.3 74.6 - - - +
121D GLY* 1.3 58.4 + - - +
122D ALA 3.7 0.2 - - - -
123D PRO* 3.5 23.4 - - + +
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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
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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