Contacts of the strand formed by residues 163 - 169 (chain A) in PDB entry 2PZX
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 TYR 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A VAL* 5.5 0.5 - - - -
68A ARG* 2.9 58.3 + - + +
125A PRO* 3.9 4.9 - - - +
143A LEU* 3.6 15.5 - - + +
147A GLY* 2.9 32.6 + - - -
149A PHE* 3.2 38.4 - + + -
158A LEU* 4.1 12.1 - - + -
159A ARG 4.2 0.7 - - - -
160A LYS* 3.5 28.1 - - + +
161A ARG 3.6 1.4 + - - -
162A GLU* 1.3 79.0 - - - +
164A CYS* 1.3 82.7 + - - +
165A LEU* 4.2 16.8 - - + -
182A PRO* 5.3 0.4 - - + -
183A HIS 3.6 14.1 - - - +
184A ASN* 4.0 10.5 - - - +
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Residues in contact with CYS 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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68A ARG* 3.3 28.5 - - - +
69A PHE 3.7 0.2 - - - -
70A CYS* 2.0 54.2 - - - +
125A PRO* 3.6 26.0 - - - -
129A MET* 4.3 6.5 - - - -
163A TYR* 1.3 82.4 - - - +
165A LEU* 1.3 63.3 + - - +
182A PRO 3.8 0.2 - - - -
183A HIS* 3.1 25.1 + - - +
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Residues in contact with LEU 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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67A VAL* 4.0 6.5 - - + -
68A ARG 2.6 17.4 + - - +
69A PHE* 3.3 13.0 - - + -
70A CYS* 3.0 19.6 + - - -
98A LEU* 3.3 29.4 - - + -
141A TYR* 5.0 2.7 - - - +
143A LEU* 3.2 34.3 - - + -
149A PHE* 4.8 3.1 - - + -
163A TYR* 4.2 13.2 - - + -
164A CYS* 1.3 74.6 - - - +
166A GLN* 1.3 70.0 + - - +
180A ILE* 3.5 11.2 - - + -
181A ALA 3.6 2.5 - - - -
182A PRO* 3.2 39.9 - - + -
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Residues in contact with GLN 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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69A PHE* 3.6 12.9 - - - -
70A CYS* 3.3 12.5 - - - +
71A CYS* 3.0 54.3 + - - +
72A PRO 3.7 2.9 - - - +
75A HIS* 2.9 25.0 - - - +
77A MET* 3.4 36.8 - - + +
165A LEU* 1.3 84.3 + - - +
167A HIS* 1.3 66.4 + - - +
168A LEU* 3.3 2.3 + - - +
180A ILE* 3.4 7.7 - - - +
181A ALA 3.0 28.4 + - - +
183A HIS* 4.6 4.5 - - - +
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Residues in contact with HIS 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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69A PHE* 4.4 7.1 - + - -
73A HIS 3.2 27.4 + - - -
75A HIS 3.6 18.6 + - - +
76A ILE* 3.2 5.1 - - - +
77A MET* 2.5 35.2 + - - +
86A MET* 3.6 14.4 - - + +
94A LEU* 3.5 31.6 - - + +
95A ASP 4.9 2.4 + - - -
112A PHE* 3.7 30.6 - + - -
166A GLN* 1.3 76.5 - - - +
168A LEU* 1.3 56.7 + - - +
178A ILE* 4.1 11.7 - - + -
180A ILE* 3.5 31.4 - - + +
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Residues in contact with LEU 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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76A ILE* 4.3 0.2 - - - -
77A MET* 4.1 14.1 - - + +
78A ASP* 6.0 0.2 - - - -
79A ASN 5.5 3.4 - - - +
131A TYR* 3.4 37.0 - - + -
166A GLN 3.3 8.5 + - - +
167A HIS* 1.3 75.2 - - - +
169A THR* 1.3 85.2 + - - +
170A PHE* 2.8 49.3 - - + -
178A ILE* 3.5 6.6 - - - +
179A ARG 3.3 18.3 + - - +
181A ALA* 4.3 4.0 - - + -
183A HIS* 3.1 37.2 - - + +
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Residues in contact with THR 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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76A ILE* 2.8 31.2 - - - +
77A MET 4.3 2.5 + - - -
90A GLU* 5.6 1.0 + - - -
168A LEU* 1.3 85.4 - - - +
170A PHE* 1.3 65.3 + - - +
176A THR* 3.4 24.2 - - - +
177A SER 3.9 4.5 - - - +
178A ILE* 3.7 10.2 - - + +
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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