Contacts of the helix formed by residues 163 - 179 (chain A) in PDB entry 1SMK
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 PRO 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A LEU* 6.5 1.3 - - + -
134A PHE* 3.7 41.5 - - + -
137A ASN* 5.3 0.9 - - + -
162A ASN* 1.3 85.6 - - + +
164A VAL* 1.3 65.9 + - - +
165A ASN* 4.5 6.3 - - + +
166A SER* 2.9 22.1 + - - +
167A THR* 2.9 17.1 + - + +
221A ALA* 5.8 8.5 - - + -
346A SER* 6.5 0.2 - - - -
349A LYS* 6.1 0.4 - - + +
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Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU 4.0 13.2 - - - +
160A ILE 3.6 19.5 - - - +
161A SER 3.8 3.4 - - - +
162A ASN* 2.8 14.0 + - - +
163A PRO* 1.3 71.2 - - - +
165A ASN* 1.3 63.8 + - - +
166A SER 3.0 1.4 + - - -
167A THR* 3.4 7.2 - - - +
168A VAL* 3.2 39.1 + - + +
188A GLY* 3.9 12.3 - - - -
189A VAL 4.3 3.8 - - - +
190A THR* 4.7 0.2 - - + -
220A HIS* 3.4 37.6 - - + +
297A PHE* 3.8 17.9 - - + -
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Residues in contact with ASN 165 (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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163A PRO* 3.2 5.8 - - + +
164A VAL* 1.3 76.5 - - - +
166A SER* 1.3 58.4 - - - +
169A PRO* 3.3 18.3 - - - +
219A GLY* 3.3 6.8 - - - -
220A HIS* 2.8 24.8 + - - +
221A ALA* 3.5 16.8 - - - +
224A THR* 3.3 31.7 + - - +
297A PHE* 3.8 14.4 - - - -
342A GLU* 5.3 1.6 + - - +
343A LEU* 3.7 13.7 - - + +
346A SER* 3.7 29.1 + - - +
347A ILE* 3.8 9.5 - - - +
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Residues in contact with SER 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE* 3.7 27.7 - - - -
163A PRO* 2.9 13.6 + - - +
165A ASN* 1.3 78.6 - - - +
167A THR* 1.3 60.1 + - - +
169A PRO* 3.0 16.0 - - - +
170A ILE* 2.9 22.5 + - - +
346A SER* 2.6 33.1 + - - -
349A LYS* 4.1 8.0 - - - +
350A GLY* 3.5 9.9 - - - -
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Residues in contact with THR 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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134A PHE* 5.4 1.6 - - + -
137A ASN 5.1 0.7 - - - +
138A ALA* 5.1 5.8 - - - +
141A VAL* 3.9 21.9 - - + +
159A LEU* 3.3 21.6 - - - +
161A SER 2.7 27.2 + - - +
162A ASN 4.1 10.8 - - - +
163A PRO* 3.3 19.6 + - + +
164A VAL* 3.4 6.1 - - - -
166A SER* 1.3 75.4 - - - +
168A VAL* 1.3 62.6 + - - +
170A ILE* 3.3 17.5 - - + +
171A ALA* 2.8 23.9 + - - +
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU* 3.9 15.7 - - + -
164A VAL* 3.2 18.1 + - + +
167A THR* 1.3 73.6 + - - +
169A PRO* 1.3 74.7 - - + +
171A ALA* 3.1 4.4 + - - +
172A ALA* 2.9 20.3 + - - +
186A LEU* 3.6 18.2 - - + +
187A LEU 4.6 0.7 - - - -
188A GLY* 3.5 32.5 - - - +
297A PHE* 3.6 21.1 - - + +
298A VAL* 5.3 0.9 - - - -
299A SER 5.6 0.2 - - - +
307A PHE* 3.7 26.2 - - + -
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Residues in contact with PRO 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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165A ASN 3.3 20.2 - - - +
166A SER 3.0 17.0 - - - +
168A VAL* 1.3 95.2 - - + +
170A ILE* 1.3 55.0 + - - +
172A ALA* 3.2 2.1 + - - +
173A GLU* 2.8 37.2 + - - +
297A PHE* 4.3 1.1 - - + -
307A PHE* 4.0 25.5 - - + -
347A ILE* 3.9 23.6 - - + +
350A GLY 4.8 0.7 - - - -
351A VAL* 3.9 26.0 - - + +
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Residues in contact with ILE 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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134A PHE* 4.3 8.7 - - + -
138A ALA* 3.7 36.1 - - + +
141A VAL* 4.2 13.7 - - + -
142A LYS 4.7 1.6 - - - +
166A SER 2.9 23.5 + - - +
167A THR* 3.3 20.6 - - + +
169A PRO* 1.3 76.8 - - - +
171A ALA* 1.3 63.2 + - - +
173A GLU* 3.3 2.9 + - - +
174A VAL* 2.9 31.4 + - + +
350A GLY* 3.3 29.6 + - - +
353A PHE* 4.3 7.9 - - + -
354A ILE* 3.8 23.3 - - + -
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Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A VAL* 4.5 0.2 - - + -
145A CYS* 3.5 30.3 - - - -
159A LEU* 3.9 11.4 - - + -
167A THR 2.8 13.6 + - - +
168A VAL 3.4 7.4 - - - +
170A ILE* 1.3 77.1 - - - +
172A ALA* 1.3 64.3 + - - +
174A VAL* 3.1 5.6 + - - +
175A PHE* 2.9 30.0 + - + -
186A LEU* 3.9 18.4 - - + -
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Residues in contact with ALA 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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168A VAL 2.9 12.7 + - - +
169A PRO 3.5 7.4 - - - +
171A ALA* 1.3 76.8 - - - +
173A GLU* 1.3 57.8 + - - +
175A PHE* 3.2 3.2 + - - +
176A LYS* 2.8 37.8 + - - +
181A TYR* 3.5 41.3 - - + +
186A LEU* 3.6 4.1 - - + +
307A PHE* 3.6 17.9 - - + -
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Residues in contact with GLU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PRO 2.8 23.3 + - - +
170A ILE 3.6 4.0 - - - +
172A ALA* 1.3 74.1 - - - +
174A VAL* 1.3 57.3 + - - +
176A LYS* 3.1 36.4 + - - +
177A LYS* 2.8 30.5 + - - +
307A PHE* 5.8 2.6 - - - -
351A VAL* 4.0 30.6 - - + +
354A ILE* 3.9 20.9 - - + +
355A ARG* 3.0 43.7 + - + +
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Residues in contact with VAL 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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142A LYS* 4.0 11.9 - - + +
145A CYS* 4.0 19.5 - - + +
146A GLU* 3.7 34.8 - - + +
149A ALA* 5.5 0.7 - - + -
170A ILE* 2.9 23.1 + - + +
171A ALA* 3.5 7.4 - - - +
173A GLU* 1.3 76.3 - - - +
175A PHE* 1.3 64.6 + - + +
177A LYS* 3.4 9.0 + - + +
178A ALA* 3.1 20.9 + - + +
354A ILE* 3.4 30.7 - - + -
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Residues in contact with PHE 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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145A CYS* 3.4 42.8 - - + -
148A ILE* 4.1 17.5 - - + -
149A ALA* 3.8 22.9 - - + -
157A VAL* 4.4 11.7 - - + -
171A ALA* 2.9 24.2 + - + -
172A ALA* 3.6 5.2 - - - +
174A VAL* 1.3 74.3 - - - +
176A LYS* 1.3 68.0 + - - +
178A ALA* 2.9 3.8 + - - +
179A GLY 2.8 19.2 + - - -
180A THR* 3.2 18.4 + - - +
181A TYR* 3.6 33.2 - + + -
182A ASP 5.7 0.4 - - - -
186A LEU* 4.0 28.3 - - + -
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Residues in contact with LYS 176 (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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172A ALA* 2.8 23.6 + - - +
173A GLU* 3.3 39.0 + - - +
175A PHE* 1.3 76.7 - - - +
177A LYS* 1.3 63.1 + - - +
179A GLY* 3.0 15.5 + - - +
181A TYR* 3.6 41.5 - - + +
307A PHE* 5.5 6.2 - - - -
355A ARG* 5.2 5.7 - - - +
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Residues in contact with LYS 177 (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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142A LYS* 6.1 0.8 - - - +
173A GLU 2.8 15.4 + - - +
174A VAL* 3.7 8.7 - - + +
175A PHE 3.2 0.2 - - - -
176A LYS* 1.3 76.8 - - - +
178A ALA* 1.3 58.7 + - - +
354A ILE* 5.0 18.6 + - + +
356A SER 5.7 2.8 + - - -
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Residues in contact with ALA 178 (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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146A GLU* 6.3 0.2 - - - -
149A ALA* 3.8 26.2 - - + -
174A VAL* 3.1 15.2 + - + +
175A PHE 2.9 6.3 + - - +
177A LYS* 1.3 77.9 - - - +
179A GLY* 1.3 63.9 + - - +
180A THR* 3.7 9.1 - - + +
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Residues in contact with GLY 179 (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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175A PHE 2.8 3.6 + - - -
176A LYS* 3.0 12.3 + - - -
177A LYS 3.5 0.4 - - - -
178A ALA* 1.3 79.8 - - - +
180A THR* 1.3 63.0 + - - +
181A TYR 3.8 1.1 - - - -
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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