Contacts of the helix formed by residues 157 - 176 (chain A) in PDB entry 6TOS
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 157 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A VAL* 3.6 12.8 - - - +
155A LYS* 5.3 1.6 - - + -
156A SER* 1.3 79.1 + - - +
158A ALA* 1.3 64.0 + - - +
159A ARG* 3.6 20.4 + - - +
160A ARG* 3.1 51.8 + - - +
161A ALA* 3.1 17.8 + - - +
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Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG 4.6 9.2 - - - +
79A THR 5.6 0.7 - - - -
80A VAL* 3.9 7.0 - - + +
83A TYR* 3.4 38.6 - - + +
157A THR* 1.3 73.8 - - - +
159A ARG* 1.4 63.6 + - + +
161A ALA* 3.3 17.8 + - - +
162A LEU* 3.5 9.6 + - - +
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Residues in contact with ARG 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A THR* 3.3 17.5 + - - +
158A ALA* 1.4 77.1 - - + +
160A ARG* 1.3 102.6 - - - +
162A LEU* 3.5 20.5 + - - +
163A GLY* 3.7 7.3 + - - -
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Residues in contact with ARG 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LYS* 3.6 55.6 + - - +
156A SER* 5.5 2.0 - - - +
157A THR* 3.1 34.6 + - - +
159A ARG* 1.3 107.2 - - - +
161A ALA* 1.4 55.0 + - - +
163A GLY* 3.4 3.0 + - - +
164A SER* 2.8 36.3 + - - +
412B SOG 3.9 24.4 - - - +
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Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 4.4 18.6 - - + -
83A TYR* 4.4 20.4 - - + -
84A PHE* 4.3 11.4 - - + -
157A THR 3.1 12.0 + - - +
158A ALA* 3.4 15.3 - - - +
159A ARG 3.3 0.4 - - - -
160A ARG* 1.4 75.9 - - - +
162A LEU* 1.4 52.4 + - - +
164A SER* 3.2 7.5 + - - -
165A ILE* 2.8 41.4 + - + +
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TYR* 4.8 15.9 - - + -
158A ALA 3.5 15.7 + - - +
159A ARG* 3.5 12.8 + - - +
160A ARG 3.4 0.6 - - - -
161A ALA* 1.4 75.6 - - - +
163A GLY* 1.3 58.8 + - - +
165A ILE* 3.8 18.6 - - + +
166A LEU* 3.0 38.6 + - + +
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Residues in contact with GLY 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ARG 3.7 6.7 + - - -
160A ARG* 3.4 6.8 + - - -
161A ALA 3.3 0.6 - - - -
162A LEU* 1.3 75.4 - - - +
164A SER* 1.4 58.3 + - - +
166A LEU* 3.6 7.7 + - - +
167A GLY 3.1 20.4 + - - -
160B ARG* 6.3 0.9 - - - -
412B SOG 3.3 38.7 + - - -
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Residues in contact with SER 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 3.8 11.2 - - - -
139A PHE* 3.7 27.6 - - - -
160A ARG* 2.8 19.9 + - - +
161A ALA* 3.6 7.4 - - - -
163A GLY* 1.4 77.0 - - - +
165A ILE* 1.4 55.7 + - - +
167A GLY* 3.3 2.3 + - - -
168A ILE* 2.9 35.3 + - - +
412B SOG 3.9 20.7 + - - +
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Residues in contact with ILE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TYR* 3.4 39.7 - - + +
84A PHE* 3.6 20.4 - - + -
87A ASN* 3.4 30.7 - - + +
90A LEU* 6.1 1.8 - - + -
161A ALA 2.8 28.0 + - - +
162A LEU* 3.8 21.1 - - + +
163A GLY 3.4 0.2 - - - -
164A SER* 1.4 68.6 - - - +
166A LEU* 1.4 66.6 + - + +
168A ILE* 3.2 16.6 + - - +
169A TRP* 3.2 25.8 + - + -
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Residues in contact with LEU 166 (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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162A LEU* 3.0 26.5 + - + +
163A GLY* 3.9 7.6 - - - +
165A ILE* 1.4 77.1 - - + +
167A GLY* 1.3 56.0 + - - +
169A TRP* 3.3 10.0 + - + +
170A ALA* 2.9 29.8 + - - +
154B PHE* 3.8 31.1 - - + -
160B ARG* 5.6 9.0 - - - +
412B SOG 5.7 1.6 - - - +
416B SOG 5.8 0.4 - - - -
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Residues in contact with GLY 167 (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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139A PHE* 5.9 1.6 - - - -
163A GLY 3.1 14.4 + - - -
164A SER 3.3 5.8 + - - -
166A LEU* 1.3 74.0 - - - +
168A ILE* 1.3 61.9 + - - +
170A ALA* 4.0 6.1 - - - +
171A VAL* 3.1 33.2 + - - +
412B SOG 4.3 19.9 + - - -
416B SOG 4.5 8.7 - - - -
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Residues in contact with ILE 168 (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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84A PHE* 3.9 16.8 - - + -
87A ASN* 4.2 2.7 - - - +
132A VAL* 3.8 32.1 - - + +
135A LEU* 3.7 27.3 - - + +
136A THR* 3.9 19.3 - - - +
139A PHE* 3.7 40.6 - - + -
164A SER 2.9 20.0 + - - +
165A ILE* 3.2 10.3 + - - +
167A GLY* 1.3 76.0 - - - +
169A TRP* 1.3 55.6 + - - +
171A VAL* 3.9 1.8 - - - +
172A SER* 2.7 36.4 + - - -
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Residues in contact with TRP 169 (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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87A ASN* 2.7 29.9 + - - +
90A LEU* 4.3 14.2 - - + +
91A ALA* 4.2 20.6 - - - -
94A LEU* 4.0 23.1 - - + -
128A VAL* 4.0 19.5 - - + -
132A VAL* 3.7 35.9 - - + -
165A ILE* 3.2 30.2 + - + +
166A LEU* 3.3 11.0 + - + +
168A ILE* 1.3 72.3 - - - +
170A ALA* 1.3 59.1 + - - +
172A SER* 3.8 2.2 - - - -
173A LEU* 2.9 49.5 + - + +
154B PHE* 4.4 11.2 - - + -
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Residues in contact with ALA 170 (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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166A LEU 2.9 17.2 + - - +
167A GLY 4.0 4.5 - - - +
168A ILE 3.4 0.2 - - - -
169A TRP* 1.3 76.0 - - - +
171A VAL* 1.3 60.4 + - - +
174A ALA* 3.4 7.8 + - - +
142B LEU* 4.0 2.0 - - + +
146B TYR* 2.6 40.5 + - + -
154B PHE* 3.7 29.5 - - + -
416B SOG 4.2 19.7 - - + -
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Residues in contact with VAL 171 (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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135A LEU* 4.1 19.7 - - + -
167A GLY* 3.1 22.4 + - - +
168A ILE 3.9 2.9 - - - +
170A ALA* 1.3 72.1 - - - +
172A SER* 1.3 60.6 + - - +
174A ALA* 3.1 3.8 + - - +
175A ILE* 3.0 52.1 + - + +
139B PHE* 4.8 16.8 - - + -
142B LEU* 3.7 27.4 - - + -
404B PGW 4.8 17.9 - - + -
412B SOG 4.9 11.4 - - + -
416B SOG 5.2 0.7 - - - -
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Residues in contact with SER 172 (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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128A VAL* 3.6 7.7 - - - +
131A SER* 2.8 32.3 + - - -
132A VAL* 3.4 31.6 + - - +
135A LEU* 3.6 4.5 - - - +
168A ILE 2.7 22.7 + - - -
169A TRP 3.8 1.8 - - - -
171A VAL* 1.3 75.6 - - - +
173A LEU* 1.3 61.4 + - - +
174A ALA 3.4 0.5 + - - -
175A ILE* 3.8 2.0 - - - +
176A MET* 3.3 30.1 + - - +
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Residues in contact with LEU 173 (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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124A TYR* 2.7 43.4 + - + +
125A LEU* 5.3 6.1 - - + -
128A VAL* 3.9 21.1 - - + -
169A TRP* 2.9 38.3 + - + +
172A SER* 1.3 72.1 - - - +
174A ALA* 1.3 61.5 + - - +
177A VAL* 3.4 12.6 + - - +
413A SOG 3.8 19.0 - - + +
146B TYR* 3.4 10.5 - - - +
153B LEU* 5.9 0.4 - - + -
154B PHE* 3.9 27.1 - - + -
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Residues in contact with ALA 174 (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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170A ALA 3.4 11.2 + - - +
171A VAL 3.1 8.8 + - - +
173A LEU* 1.3 76.3 - - - +
175A ILE* 1.3 61.8 + - + +
176A MET 3.2 4.7 - - - -
177A VAL* 3.2 17.5 + - - +
142B LEU* 3.6 19.5 - - + -
145B TRP* 3.5 30.3 - - + -
146B TYR* 3.7 0.4 + - - -
404B PGW 3.3 26.7 - - + +
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Residues in contact with ILE 175 (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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131A SER* 3.6 19.5 - - - +
135A LEU* 5.1 2.9 - - + -
171A VAL* 3.0 34.5 + - + +
172A SER* 3.8 7.6 - - - +
174A ALA* 1.3 75.1 - - + +
176A MET* 1.4 71.8 + - + +
177A VAL 3.4 0.4 - - - -
178A PRO* 3.3 16.7 - - - +
215A TYR* 5.2 1.4 + - - -
222A VAL* 5.0 9.6 - - + -
223A THR* 5.7 0.7 - - + -
142B LEU* 5.7 0.2 - - + -
230B LEU* 3.8 38.6 - - + +
404B PGW 4.0 55.4 - - + +
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Residues in contact with MET 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A TYR* 3.3 12.9 - - + -
127A ALA* 3.6 38.4 - - + +
128A VAL* 3.7 17.3 - - + +
131A SER* 3.6 24.9 - - - +
172A SER 3.3 19.9 + - - +
173A LEU 4.1 0.2 + - - -
174A ALA 3.2 1.0 - - - -
175A ILE* 1.4 84.0 - - + +
177A VAL* 1.4 63.6 + - - +
178A PRO* 3.4 2.2 - - - -
179A GLN* 3.2 20.1 + - - +
180A ALA 3.3 4.0 + - - -
215A TYR* 4.7 5.4 - - - -
219A PHE* 3.6 28.0 - - + -
223A THR* 3.8 14.6 - - + -
404B PGW 4.0 12.8 - - + -
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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