Contacts of the helix formed by residues 107 - 120 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B LEU* 6.0 1.8 - - + -
75B ILE* 6.3 4.3 - - + -
103B VAL* 2.8 30.9 + - + +
106B ASP* 1.3 77.4 - - + +
108B PRO* 1.3 62.9 - - - +
109B GLN* 3.2 10.1 - - - +
110B ALA* 3.0 29.3 + - + +
111B SER* 3.4 4.3 + - - -
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Residues in contact with PRO 108 (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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104B SER 3.4 17.0 - - - +
105B ARG 3.6 11.9 - - - +
106B ASP 3.2 9.9 - - - +
107B TYR* 1.3 91.5 - - - +
109B GLN* 1.3 65.5 + - - +
111B SER* 3.1 4.0 + - - -
112B ARG* 2.9 48.0 + - + +
173B ALA* 3.9 18.8 - - + +
188B ARG* 6.3 0.7 - - - +
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Residues in contact with GLN 109 (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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27B LEU* 3.9 14.5 - - + +
28B ASP* 3.7 27.4 + - - +
31B SER* 3.9 15.5 - - - +
106B ASP 4.2 2.5 + - - +
107B TYR* 3.3 10.1 - - - -
108B PRO* 1.3 95.5 - - - +
110B ALA* 1.3 64.1 + - - +
112B ARG* 3.4 29.7 + - - +
113B LEU* 3.0 24.8 + - - +
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Residues in contact with ALA 110 (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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27B LEU* 3.9 15.3 - - + -
72B ILE* 3.1 46.1 - - + +
76B TRP* 5.7 0.2 - - + -
103B VAL* 5.8 3.1 - - + -
107B TYR* 3.0 23.6 + - + +
109B GLN* 1.3 83.1 - - - +
111B SER* 1.3 62.4 + - - +
113B LEU* 3.4 0.3 + - - +
114B PHE* 3.1 20.4 + - - +
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Residues in contact with SER 111 (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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76B TRP* 3.8 23.5 - - - +
103B VAL* 6.3 0.7 - - - -
104B SER* 5.2 5.4 - - - -
107B TYR 3.4 2.2 + - - -
108B PRO* 3.1 13.0 + - - -
110B ALA* 1.3 79.3 - - - +
112B ARG* 1.3 63.2 + - - +
114B PHE* 3.3 3.8 + - - +
115B CYS* 3.0 23.0 + - - +
170B GLN* 4.1 13.8 + - - +
173B ALA* 3.5 16.2 - - - +
174B ASP* 2.4 28.5 + - - +
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Residues in contact with ARG 112 (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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118A MSE 5.4 0.9 - - - -
119A LEU* 3.9 37.4 + - + +
31B SER* 4.6 6.4 + - - -
32B GLN* 3.8 22.6 - - - +
108B PRO* 2.9 33.8 + - - +
109B GLN* 3.7 38.7 - - - +
111B SER* 1.3 76.1 - - - +
113B LEU* 1.3 56.2 + - - +
115B CYS* 3.1 4.2 + - - +
116B MSE 2.8 45.8 + - + +
173B ALA 4.4 16.6 + - - +
174B ASP* 4.0 12.1 - - - +
177B PRO* 6.5 0.4 - - - -
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Residues in contact with LEU 113 (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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27B LEU* 3.8 15.3 - - + +
30B PHE* 3.5 48.7 - - + +
31B SER* 3.6 6.0 - - - +
34B GLY* 5.4 2.2 - - - -
65B TYR* 4.2 17.7 - - + +
68B VAL* 3.5 31.9 - - + -
69B LEU* 4.2 11.6 - - + +
72B ILE* 4.7 0.9 - - + -
109B GLN 3.0 17.3 + - - +
110B ALA 3.8 3.4 - - - +
112B ARG* 1.3 72.3 - - - +
114B PHE* 1.3 67.4 + - - +
116B MSE 3.1 17.2 + - + +
117B GLU* 3.1 22.7 + - - +
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Residues in contact with PHE 114 (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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175A PHE* 3.9 9.0 - + - -
178A GLN* 3.5 26.5 - - - -
69B LEU* 3.9 21.2 - - + +
72B ILE* 4.8 5.8 - - + -
73B LEU* 3.8 21.3 - - + -
76B TRP* 3.6 28.5 - + + -
110B ALA 3.1 11.3 + - - +
111B SER 3.3 8.3 + - - +
113B LEU* 1.3 76.1 - - - +
115B CYS* 1.3 63.5 + - - +
117B GLU* 3.4 4.7 + - - +
118B MSE 3.2 46.0 + - + +
125B LEU* 3.5 31.2 - - + -
129B LEU* 4.4 2.9 - - + -
212B URA 3.9 14.6 - - - -
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Residues in contact with CYS 115 (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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115A CYS* 3.9 20.0 - - - -
119A LEU* 3.8 17.3 - - + -
175A PHE* 3.8 22.0 - - + -
111B SER 3.0 13.3 + - - +
112B ARG 3.3 8.5 - - - +
114B PHE* 1.3 76.0 - - - +
116B MSE 1.3 64.7 + - - +
118B MSE 3.0 11.2 + - - +
119B LEU* 3.0 29.9 + - - +
174B ASP* 3.5 26.0 - - - +
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Residues in contact with MSE 116 (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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119A LEU* 3.7 40.6 - - + +
120A ALA* 5.8 0.4 - - - -
30B PHE 4.4 3.1 - - - +
31B SER* 2.9 31.2 - - - +
32B GLN 5.7 0.9 - - - +
34B GLY* 5.4 6.1 - - - -
65B TYR* 5.5 1.1 - - - +
112B ARG* 2.8 34.0 + - + +
113B LEU* 3.4 28.7 - - + +
115B CYS* 1.3 71.7 - - - +
117B GLU* 1.3 62.9 + - - +
119B LEU* 3.0 17.8 + - - +
120B ALA* 3.1 14.3 + - - +
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Residues in contact with GLU 117 (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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35B PHE* 5.7 0.7 - - - +
65B TYR* 2.6 44.0 + - - +
69B LEU* 3.7 19.1 - - + -
113B LEU 3.1 6.1 + - - +
114B PHE 3.5 9.6 - - - +
116B MSE 1.3 76.2 - - - +
118B MSE 1.3 58.7 + - - +
120B ALA* 3.5 4.7 + - - +
121B GLY 3.5 2.9 + - - -
122B ALA* 2.7 41.9 + - + -
123B PRO* 3.6 12.3 - - - +
124B LEU* 2.8 30.9 + - - +
125B LEU* 3.1 22.1 + - + -
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Residues in contact with MSE 118 (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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112A ARG* 5.1 2.6 + - - -
174A ASP 3.5 14.1 - - - +
175A PHE* 3.7 24.2 - - + +
177A PRO* 3.0 59.1 - - + +
178A GLN* 3.3 20.9 - - - +
114B PHE* 3.2 42.1 + - + +
115B CYS* 3.0 9.7 + - - +
117B GLU* 1.3 77.7 - - - +
119B LEU* 1.3 59.7 + - - +
121B GLY* 2.9 21.3 + - - -
122B ALA* 4.2 5.2 - - + +
125B LEU* 5.8 0.9 - - - -
129B LEU* 4.1 14.4 - - - -
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Residues in contact with LEU 119 (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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112A ARG* 3.6 35.1 + - + +
115A CYS* 3.9 11.4 - - + -
116A MSE 3.3 57.5 - - + +
119A LEU* 3.7 25.8 - - + -
174A ASP* 3.7 35.2 - - + +
115B CYS* 3.0 19.3 + - - +
116B MSE 3.0 9.1 + - - +
118B MSE 1.3 77.2 - - - +
120B ALA* 1.3 58.6 + - - +
121B GLY 3.2 0.9 + - - -
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Residues in contact with ALA 120 (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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116A MSE 5.1 4.9 - - + -
116B MSE 3.1 13.2 + - - +
117B GLU* 4.0 8.5 - - - +
118B MSE 3.1 0.4 - - - -
119B LEU* 1.3 75.4 - - - +
121B GLY* 1.3 57.3 + - - +
122B ALA 3.7 0.2 - - - -
123B PRO* 3.6 24.0 - - + +
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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