Contacts of the helix formed by residues 162 - 174 (chain A) in PDB entry 4ZTF
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 SER 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A TYR* 3.4 1.2 + - - -
160A ALA* 2.8 22.0 + - - +
161A PRO* 1.4 72.1 - - - +
163A THR* 1.4 59.3 + - - +
164A SER* 3.1 14.4 + - - -
165A ALA* 3.1 16.3 + - - +
166A THR* 2.7 32.4 + - - -
189A ALA* 3.6 5.4 - - - +
402A GOL 3.5 24.5 - - - -
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Residues in contact with THR 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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162A SER* 1.4 69.9 - - - +
164A SER* 1.4 58.2 + - - +
166A THR* 3.1 5.2 + - - -
167A VAL* 2.9 34.1 + - + +
188A ALA 4.0 0.7 + - - -
189A ALA* 2.7 27.3 + - - +
192A SER* 2.7 31.3 + - - +
194A THR* 3.9 17.3 - - + -
195A PHE* 3.7 24.9 - - + +
402A GOL 3.0 22.2 + - - +
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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
----------------------------------------------------------
162A SER* 3.1 6.2 + - - -
163A THR* 1.4 79.1 - - - +
165A ALA* 1.3 57.7 + - - +
167A VAL* 3.6 6.3 + - - +
168A LYS* 3.1 46.2 + - - +
194A THR* 6.5 0.2 - - - -
402A GOL 2.9 37.3 + - - -
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TYR* 3.8 3.8 - - - +
158A THR* 3.8 29.8 - - + -
159A LYS 5.4 1.8 - - - +
160A ALA 4.0 5.2 - - - +
162A SER* 3.1 17.2 + - - +
163A THR 3.3 0.2 - - - -
164A SER* 1.3 77.4 + - - +
166A THR* 1.4 60.1 + - - +
168A LYS* 3.9 9.8 - - - +
169A SER* 2.8 34.0 + - - -
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Residues in contact with THR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 4.2 1.3 - - + -
129A TYR* 2.7 21.8 + - - -
143A LEU* 4.2 13.2 - - + -
162A SER 2.7 20.2 + - - -
163A THR* 3.1 9.6 + - - -
165A ALA* 1.4 74.9 - - - +
167A VAL* 1.3 55.0 + - - +
169A SER* 3.3 2.1 + - - -
170A LEU* 2.8 51.2 + - + +
189A ALA* 3.9 3.8 - - - +
190A PHE* 3.8 20.2 - - + -
195A PHE* 3.7 25.6 - - + -
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A THR* 2.9 27.7 + - + +
164A SER* 3.8 6.7 - - - +
166A THR* 1.3 74.8 - - - +
168A LYS* 1.3 57.8 + - + +
170A LEU* 3.3 3.8 + - - +
171A ASN* 2.9 46.0 + - - +
194A THR* 4.9 6.5 - - + +
195A PHE* 4.1 13.7 - - + -
198A TRP* 3.6 45.3 - - + +
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Residues in contact with LYS 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 SER* 3.1 34.4 + - - +
165A ALA* 3.9 8.5 - - - +
166A THR 3.4 0.2 - - - -
167A VAL* 1.3 78.3 - - + +
169A SER* 1.4 61.7 + - - +
171A ASN* 3.5 8.5 + - - +
172A VAL* 3.5 24.1 + - - +
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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
----------------------------------------------------------
143A LEU* 3.6 18.2 - - - +
156A TYR* 3.5 49.3 - - - +
157A PRO 5.4 0.3 + - - -
158A THR* 4.3 6.2 - - - +
165A ALA 2.8 23.6 + - - -
168A LYS* 1.4 75.8 - - - +
170A LEU* 1.4 56.5 + - - +
172A VAL* 3.1 11.1 + - - +
173A LEU 3.1 21.7 + - - -
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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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125A PHE* 5.1 2.7 - - + -
127A ILE* 4.2 10.8 - - + -
143A LEU* 4.6 4.0 - - + -
145A VAL* 4.1 29.6 - - + -
166A THR* 2.8 30.5 + - + +
167A VAL 4.1 0.9 - - - +
169A SER* 1.4 70.0 - - - +
171A ASN* 1.3 56.0 + - - +
173A LEU* 4.2 15.3 - - + -
174A THR* 2.8 40.3 + - + +
182A ILE* 4.1 14.1 - - + -
195A PHE* 3.7 35.4 - - + -
198A TRP* 3.6 26.5 - - + -
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Residues in contact with ASN 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 VAL* 2.9 36.0 + - - +
168A LYS* 3.7 8.7 - - - +
169A SER 3.3 0.2 - - - -
170A LEU* 1.3 74.5 - - - +
172A VAL* 1.4 58.3 + - + +
174A THR* 3.7 8.6 + - - -
175A SER* 3.0 17.3 + - - -
198A TRP* 2.7 25.5 + - - +
202A ARG* 3.3 20.3 + - - +
247B PRO* 3.5 22.4 - - + +
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Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TYR* 4.4 15.9 - - + +
168A LYS 3.5 14.4 - - - +
169A SER* 3.1 10.2 + - - +
171A ASN* 1.4 76.1 - - + +
173A LEU* 1.3 65.8 + - - +
175A SER* 3.1 21.1 + - - -
176A ILE* 4.5 4.0 + - - +
156B TYR* 6.2 3.4 - - + -
172B VAL* 5.6 10.3 - - + -
243B TYR* 5.7 4.5 - - - +
247B PRO* 5.6 0.2 - - - -
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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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122A PHE* 5.3 0.9 - - + -
125A PHE* 4.0 19.3 - - + -
145A VAL* 3.5 44.2 - - + -
154A TRP* 3.5 44.9 - - + +
156A TYR* 3.2 21.7 + - + +
169A SER 3.1 9.2 + - - +
170A LEU* 3.4 14.6 + - + +
172A VAL* 1.3 77.3 - - - +
174A THR* 1.4 56.4 + - + +
175A SER 2.9 7.0 + - - -
176A ILE* 3.0 23.7 + - + +
177A ALA 4.1 3.3 + - - +
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Residues in contact with THR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A PHE* 5.4 1.6 - - + -
170A LEU* 2.8 35.1 + - + +
171A ASN* 3.7 12.2 + - - -
172A VAL 3.4 0.2 - - - -
173A LEU* 1.4 70.6 - - + +
175A SER* 1.3 61.1 + - - +
176A ILE 3.1 2.6 + - - -
177A ALA 3.3 10.4 - - - +
178A ILE* 3.8 15.7 - - + +
179A PRO* 4.1 26.0 - - + -
182A ILE* 5.8 0.2 - - + -
198A TRP* 4.3 20.7 - - + -
202A ARG* 4.7 4.9 + - - -
204A ILE* 4.5 2.2 - - + -
247B PRO* 5.0 3.1 - - - +
251B LEU* 3.4 26.2 - - - +
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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