Contacts of the strand formed by residues 171 - 175 (chain A) in PDB entry 1ZQ1
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 171 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLU 3.7 1.8 + - - +
94A VAL* 3.2 26.6 - - - +
95A THR 3.6 2.3 + - - -
165A LEU* 3.8 7.0 - - - -
169A ASP* 3.3 2.6 - - - +
170A TYR* 1.3 79.8 - - - +
172A VAL* 1.3 66.4 + - - +
198A PRO* 3.6 8.7 - - - -
226A ALA* 3.5 24.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 5.3 0.4 - - - -
95A THR* 3.6 28.5 - - + +
97A ILE* 3.8 28.7 - - + -
161A VAL* 4.0 31.6 - - + +
164A ALA* 4.5 0.4 - - + -
165A LEU* 3.4 27.1 - - + +
169A ASP* 4.8 0.4 - - + -
171A GLY* 1.3 74.8 - - - +
173A VAL* 1.3 75.6 + - - +
174A VAL* 4.4 2.9 - - + -
198A PRO 2.9 14.4 + - - +
199A VAL* 4.9 2.5 - - + -
200A VAL* 3.0 22.4 + - - +
226A ALA* 4.0 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 5.3 4.2 - - + +
95A THR 3.2 5.4 + - - +
96A ILE* 3.1 30.5 - - + +
97A ILE 3.0 21.3 + - - -
172A VAL* 1.3 81.9 - - - +
174A VAL* 1.3 64.4 + - - +
175A ALA* 4.9 1.3 - - + +
200A VAL* 3.4 15.5 - - + +
202A VAL* 4.7 4.5 - - + -
219A LEU* 4.5 8.3 - - + -
222A SER* 3.9 31.9 - - - +
223A VAL* 4.2 7.9 - - + -
226A ALA* 3.5 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ILE* 3.5 12.3 - - + +
99A THR* 3.2 29.6 - - + +
157A ILE* 4.4 13.5 - - + -
161A VAL* 4.0 26.9 - - + -
172A VAL* 4.4 4.0 - - + -
173A VAL* 1.3 72.8 - - - +
175A ALA* 1.3 58.0 + - - +
176A HIS* 3.2 6.8 + - + +
184A THR* 5.5 0.7 - - + -
188A LEU* 4.5 5.2 - - + -
199A VAL* 4.6 7.2 - - + -
200A VAL 2.8 8.8 + - - +
201A LEU* 3.3 31.3 - - + -
202A VAL* 2.8 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ILE* 4.1 14.8 - - + -
97A ILE 2.9 13.6 + - - +
98A GLY* 4.5 5.6 - - - -
99A THR* 3.1 16.6 + - - -
101A GLY 3.1 32.4 + - - +
103A ILE* 3.6 22.7 - - + -
118A PHE* 4.6 2.9 - - + -
173A VAL* 3.7 3.8 + - + -
174A VAL* 1.3 68.0 - - - +
176A HIS* 1.3 60.1 + - - +
202A VAL* 3.3 8.5 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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