Contacts of the helix formed by residues 147 - 164 (chain P) in PDB entry 1SVC
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 LYS 147 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D A 3.3 52.9 + - - +
11D T 2.8 14.8 + - - +
146P THR* 1.3 70.5 - - - +
148P LYS* 1.3 64.4 + - + +
149P LYS 3.1 1.6 + - - -
150P VAL* 3.2 25.9 + - + +
210P LEU* 3.9 23.4 - - + +
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Residues in contact with LYS 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D T 4.5 0.8 + - - +
146P THR* 3.2 8.1 + - - +
147P LYS* 1.3 79.8 - - + +
149P LYS* 1.3 61.2 + - + +
150P VAL 3.5 0.2 - - - -
151P PHE 5.6 0.2 + - - -
152P GLU* 4.6 4.7 - - - +
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Residues in contact with LYS 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145P VAL* 3.9 9.9 - - + -
146P THR* 3.1 23.6 + - - +
148P LYS* 1.3 80.4 - - + +
150P VAL* 1.3 63.4 + - - +
151P PHE 3.5 2.2 - - - -
152P GLU* 3.6 30.5 - - + +
153P THR* 3.0 27.5 + - - +
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Residues in contact with VAL 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111P ALA* 4.2 4.5 - - + +
145P VAL* 4.2 9.9 - - + -
146P THR 3.1 17.7 - - - +
147P LYS* 3.2 22.0 + - + +
148P LYS 3.5 0.8 - - - -
149P LYS* 1.3 76.9 - - - +
151P PHE* 1.3 58.0 + - - +
153P THR* 3.4 1.9 + - - -
154P LEU* 2.9 28.2 + - - +
205P THR* 3.6 27.6 - - + +
208P MET* 4.0 25.8 - - + -
210P LEU* 3.9 22.7 - - + -
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Residues in contact with PHE 151 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148P LYS 5.6 0.2 + - - -
149P LYS 3.5 0.8 - - - -
150P VAL* 1.3 77.4 - - - +
152P GLU* 1.3 72.4 + - + +
153P THR 3.0 0.5 + - - -
154P LEU* 3.0 2.9 + - - +
155P GLU* 2.9 54.6 + - - +
198P ARG* 3.6 28.7 - - + -
201P ALA* 3.3 29.6 - - + -
202P LEU* 3.4 40.6 - - + -
205P THR* 3.3 21.0 - - + +
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Residues in contact with GLU 152 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148P LYS 4.6 3.7 - - - +
149P LYS* 3.6 45.8 - - + +
151P PHE* 1.3 85.1 - - + +
153P THR* 1.3 59.8 + - - +
155P GLU* 4.1 8.4 - - - +
156P ALA* 3.5 20.1 + - - +
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Residues in contact with THR 153 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111P ALA* 3.3 13.7 - - - +
145P VAL* 3.7 17.7 - - + +
149P LYS* 3.0 23.4 + - - +
150P VAL 3.9 2.5 - - - -
151P PHE 3.0 1.0 - - - -
152P GLU* 1.3 76.7 - - - +
154P LEU* 1.3 66.3 + - - +
155P GLU 3.2 1.3 - - - -
156P ALA* 3.2 6.5 + - + +
157P ARG* 3.0 53.7 + - - +
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Residues in contact with LEU 154 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109P LEU* 3.8 24.2 - - + +
110P HIS 4.7 4.5 - - - +
111P ALA* 4.4 8.9 - - + +
150P VAL 2.9 17.9 + - - +
151P PHE 3.5 3.6 - - - +
153P THR* 1.3 75.3 - - - +
155P GLU* 1.3 63.4 + - - +
157P ARG* 3.3 4.4 + - + +
158P MET* 3.0 44.7 + - + +
201P ALA* 3.7 13.2 - - + +
204P GLN* 3.7 22.0 - - + +
205P THR* 3.4 25.1 - - + -
208P MET* 3.6 25.1 - - + -
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Residues in contact with GLU 155 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151P PHE* 2.9 47.9 + - - +
152P GLU* 4.2 7.0 - - - +
154P LEU* 1.3 77.6 - - - +
156P ALA* 1.3 55.9 + - - +
158P MET* 3.2 7.0 + - - +
159P THR* 2.9 34.6 + - - +
194P LYS 5.4 1.2 - - - +
197P ILE* 3.6 17.0 - - + +
198P ARG* 3.8 22.6 + - - +
201P ALA* 3.8 18.5 - - + +
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Residues in contact with ALA 156 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152P GLU 3.5 18.1 + - - +
153P THR* 3.2 7.9 + - + +
155P GLU* 1.3 79.0 - - - +
157P ARG* 1.3 66.8 + - - +
159P THR* 3.6 8.3 + - - -
160P GLU* 3.3 24.4 + - - +
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Residues in contact with ARG 157 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109P LEU* 3.7 23.4 - - + +
110P HIS 3.9 15.7 - - - +
111P ALA 3.0 20.4 + - - -
112P HIS 3.5 16.7 + - - -
113P SER* 2.6 27.7 + - - -
121P ASP* 4.1 25.4 + - - +
122P GLY* 4.3 10.0 - - - -
123P ILE* 5.4 5.4 - - + +
153P THR* 3.0 27.4 + - - +
154P LEU* 3.5 10.1 - - + +
155P GLU 3.2 0.2 - - - -
156P ALA* 1.3 79.4 - - - +
158P MET* 1.3 65.0 + - - +
160P GLU* 3.6 6.5 + - - +
161P ALA* 3.3 17.3 + - - +
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Residues in contact with MET 158 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109P LEU* 3.7 15.5 - - + -
154P LEU* 3.0 30.7 + - + +
155P GLU 3.5 4.9 - - - +
157P ARG* 1.3 74.5 - - - +
159P THR* 1.3 66.8 + - - +
161P ALA* 3.2 3.6 + - - +
162P CYS* 3.0 25.6 + - - +
171P LEU 3.8 3.8 - - - +
172P VAL* 3.5 43.8 - - + +
197P ILE* 3.5 21.3 - - + +
200P ALA* 3.5 9.0 - - + -
201P ALA* 3.8 23.1 - - - -
204P GLN* 3.0 28.3 - - - +
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Residues in contact with THR 159 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155P GLU* 2.9 19.0 + - - +
156P ALA* 3.6 12.7 - - - -
158P MET* 1.3 76.9 - - - +
160P GLU* 1.3 65.4 + - + +
162P CYS* 3.1 3.6 + - - +
163P ILE* 3.0 43.5 + - + +
189P LEU* 3.8 13.0 - - + -
197P ILE* 3.7 21.6 - - - +
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Residues in contact with GLU 160 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121P ASP* 3.2 26.4 - - + +
123P ILE* 5.4 4.3 - - + -
156P ALA 3.3 14.0 + - - +
157P ARG* 3.9 6.3 - - - +
158P MET 3.3 0.6 - - - -
159P THR* 1.3 80.4 - - + +
161P ALA* 1.3 51.1 + - - +
163P ILE* 3.0 19.4 + - + +
164P ARG* 2.7 81.4 + - - +
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Residues in contact with ALA 161 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99P GLN* 4.0 12.6 - - - +
109P LEU* 4.2 12.1 - - + -
123P ILE* 5.1 7.7 - - + +
157P ARG 3.3 13.5 + - - +
158P MET 3.2 5.4 + - - +
160P GLU* 1.3 77.6 - - - +
162P CYS* 1.3 54.5 + - - +
164P ARG* 3.6 7.9 - - - +
165P GLY* 2.8 9.7 + - - -
166P TYR* 2.7 48.2 + - + +
168P PRO* 4.0 8.4 - - + +
171P LEU* 5.2 0.2 - - + -
172P VAL* 5.6 1.3 - - + -
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Residues in contact with CYS 162 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158P MET 3.0 11.1 + - - +
159P THR 3.2 9.6 - - - +
161P ALA* 1.3 76.2 - - - +
163P ILE* 1.3 59.0 + - - +
165P GLY 3.4 2.8 + - - -
168P PRO* 3.9 19.5 - - - -
172P VAL* 4.4 7.0 - - - -
176P LEU* 3.6 25.6 - - - -
179P LEU* 3.9 17.1 - - + +
182P GLU 3.1 19.8 - - - +
183P GLY* 3.8 3.6 - - - -
189P LEU* 3.9 16.4 - - + -
197P ILE* 3.5 26.5 - - + -
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Residues in contact with ILE 163 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159P THR* 3.0 34.3 + - + +
160P GLU* 3.4 23.3 - - + +
162P CYS* 1.3 79.3 - - - +
164P ARG* 1.3 60.0 + - + +
182P GLU 3.7 4.0 - - - +
183P GLY* 4.0 7.0 - - - -
184P GLY 3.6 16.2 + - - +
185P GLY* 3.2 29.0 + - - +
186P ASP* 3.4 24.9 - - + +
189P LEU* 3.8 27.1 - - + -
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Residues in contact with ARG 164 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120P GLU* 2.9 47.2 + - - +
121P ASP* 3.7 13.1 + - - +
123P ILE* 3.1 31.7 - - - +
125P THR* 5.7 2.2 + - - -
160P GLU* 2.7 54.7 + - - +
161P ALA* 4.2 1.8 - - - +
163P ILE* 1.3 75.5 - - + +
165P GLY* 1.3 61.1 + - - +
166P TYR* 3.3 45.6 - - + -
181P ALA* 4.7 5.7 - - - -
182P GLU 4.1 3.5 + - - -
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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
------------------------------------------------------------
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