Contacts of the helix formed by residues 162 - 171 (chain A) in PDB entry 5K9S
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 GLY 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A VAL* 3.8 10.4 - - - +
159A VAL 3.0 12.2 + - - -
160A ASP 3.1 3.8 + - - -
161A GLY* 1.3 77.7 - - - +
163A ALA* 1.3 63.4 + - - +
164A ILE 3.3 2.7 - - - -
165A PRO* 3.3 20.6 - - - +
166A ALA* 3.9 4.5 + - - +
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Residues in contact with ALA 163 (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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125A VAL* 3.8 22.4 - - + -
128A LEU* 5.1 0.2 - - + -
144A LEU* 4.8 0.9 - - + -
158A VAL* 3.2 40.2 + - + +
159A VAL 4.1 1.2 + - - -
161A GLY 3.4 0.8 - - - -
162A GLY* 1.3 78.5 - - - +
164A ILE* 1.3 65.7 + - - +
166A ALA* 3.2 3.5 + - - +
167A PHE* 2.9 41.3 + - + -
189A ILE* 4.9 2.0 - - + -
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Residues in contact with ILE 164 (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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159A VAL* 4.1 24.0 + - + -
163A ALA* 1.3 77.5 - - - +
165A PRO* 1.3 71.7 - - + +
167A PHE* 3.2 3.0 + - - +
168A ILE* 2.9 34.0 + - + +
186A LEU* 4.2 11.8 - - + +
189A ILE* 4.0 37.7 - - + -
196A PHE* 5.9 0.2 - - + -
199A LEU* 4.0 22.2 - - + -
200A VAL* 4.0 18.8 - - + -
203A HIS* 3.7 27.1 - - + +
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Residues in contact with PRO 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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162A GLY* 3.3 18.2 - - - +
164A ILE* 1.3 96.5 - - + +
166A ALA* 1.3 56.5 + - - +
168A ILE* 3.3 9.4 + - + +
169A SER* 2.9 32.9 + - - +
203A HIS* 3.4 32.8 - - + +
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Residues in contact with ALA 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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125A VAL* 4.2 19.5 - - + +
128A LEU* 3.6 32.5 - - + +
129A GLY* 5.5 0.7 - - - +
162A GLY 3.9 1.7 + - - +
163A ALA 3.2 8.4 + - - +
164A ILE 3.1 1.2 - - - -
165A PRO* 1.3 79.6 - - - +
167A PHE* 1.3 62.8 + - - +
169A SER* 3.3 9.2 + - - -
170A LEU* 3.2 23.7 + - - +
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Residues in contact with PHE 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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128A LEU* 3.8 20.9 - - + -
141A ALA* 3.8 23.1 - - + -
144A LEU* 3.8 28.0 - - + -
158A VAL* 4.7 1.8 - - + -
163A ALA* 2.9 45.4 + - + +
164A ILE* 3.8 3.4 - - - +
166A ALA* 1.3 71.5 - - - +
168A ILE* 1.3 68.0 + - - +
170A LEU* 2.9 17.1 + - + +
171A LEU* 3.2 10.0 + - - +
182A ALA* 3.6 26.9 - - + +
185A ALA* 3.5 30.1 - - + -
186A LEU* 3.9 19.7 - - + -
189A ILE* 4.4 14.6 - - + -
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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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164A ILE* 2.9 24.6 + - + +
165A PRO* 3.6 9.0 - - + +
167A PHE* 1.3 75.0 - - - +
169A SER* 1.3 63.8 + - - +
171A LEU* 3.1 25.1 + - + +
172A ALA* 4.4 0.9 + - - +
186A LEU* 4.2 9.6 - - + -
200A VAL 4.1 0.4 - - - +
203A HIS* 3.3 47.6 - - + +
204A GLY 4.2 5.4 - - - +
205A ALA* 3.9 24.9 - - + +
208A PRO* 4.2 22.8 - - + +
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Residues in contact with SER 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 PRO* 2.9 16.0 + - - +
166A ALA* 3.4 11.3 - - - -
168A ILE* 1.3 78.0 - - - +
170A LEU* 1.3 62.9 + - - +
171A LEU 3.3 0.7 + - - -
172A ALA* 3.4 17.0 + - - +
173A SER 4.4 0.9 + - - -
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Residues in contact with LEU 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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128A LEU* 3.5 41.7 - - + +
137A GLN* 3.4 35.9 - - + +
141A ALA* 4.9 4.3 - - + -
166A ALA 3.2 10.1 + - - +
167A PHE* 2.9 19.0 + - + +
169A SER* 1.3 75.6 - - - +
171A LEU* 1.3 64.2 + - - +
172A ALA 3.0 3.4 - - - -
173A SER* 2.9 26.2 + - - +
178A ILE* 4.0 22.7 - - + -
179A SER* 3.7 7.8 - - - -
182A ALA* 3.9 11.2 - - + -
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Residues in contact with LEU 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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167A PHE 3.2 7.4 + - - +
168A ILE* 3.1 19.6 + - + +
170A LEU* 1.3 75.9 - - - +
172A ALA* 1.3 55.9 + - - +
173A SER 3.3 0.7 + - - +
179A SER* 3.1 20.6 + - - +
182A ALA* 4.1 4.5 - - + -
183A VAL* 3.4 43.3 - - + +
186A LEU* 4.0 15.5 - - + -
205A ALA 4.2 2.0 - - - +
208A PRO* 3.8 37.0 - - + -
209A LEU* 3.9 25.4 - - + +
212A LEU* 3.6 22.2 - - + +
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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