Contacts of the strand formed by residues 169 - 178 (chain A) in PDB entry 4ZDH
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 PHE 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A ASN 5.9 2.5 - - - -
139A ASP* 4.4 8.7 - - - -
162A LEU 3.9 0.2 - - - +
163A ASP* 3.7 2.7 + - - +
164A MET* 2.8 45.4 + - + +
167A MET* 3.2 21.5 - - + +
168A ASP* 1.3 77.8 - - - +
170A LYS* 1.3 72.2 + - - +
171A SER* 3.7 15.0 - - - -
137B THR* 6.5 0.2 - - - -
139B LYS* 3.8 35.9 - - + -
194B ARG* 3.5 29.6 - - - -
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Residues in contact with LYS 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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16A GLU* 3.2 27.0 + - - +
81A GLN* 6.2 0.2 - - - -
82A PRO* 4.0 27.6 - - + -
112A PRO* 4.1 20.0 - - + -
113A ASP 5.9 1.8 - - - +
114A ILE* 4.0 13.7 - - + +
161A VAL* 4.8 4.9 - - + -
162A LEU 3.2 8.7 - - - +
163A ASP* 3.3 33.7 - - + +
168A ASP* 4.9 10.6 + - - -
169A PHE* 1.3 90.1 - - - +
171A SER* 1.3 64.8 + - - +
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Residues in contact with SER 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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114A ILE* 4.5 6.1 - - - -
138A THR* 4.6 1.4 + - - -
139A ASP* 3.5 26.7 - - - +
160A CYS 3.6 1.7 - - - +
161A VAL* 3.6 3.7 - - - +
162A LEU* 3.0 48.2 + - - +
169A PHE* 3.7 9.9 - - - -
170A LYS* 1.3 76.9 - - - +
172A ASN* 1.3 64.4 + - - +
173A SER* 5.4 0.9 + - - -
194B ARG* 3.1 18.8 + - - -
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Residues in contact with ASN 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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112A PRO* 3.6 8.7 - - - +
114A ILE* 3.6 9.5 - - - +
138A THR* 3.2 2.9 + - - -
139A ASP* 2.9 27.2 + - - +
140A PHE* 2.9 50.0 + - + +
141A ASP 3.8 0.4 - - - -
142A SER* 3.3 28.3 + - - +
159A LYS* 4.8 11.7 + - + +
160A CYS 3.5 4.8 - - - +
161A VAL* 3.5 23.6 - - - +
171A SER* 1.3 74.1 - - - +
173A SER* 1.3 62.7 + - - +
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Residues in contact with SER 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 3.9 9.2 - - - -
137A PHE 3.1 13.7 - - - -
138A THR* 3.5 15.3 - - - -
140A PHE* 3.7 6.5 - - - -
159A LYS* 3.1 4.2 - - - -
160A CYS 2.9 33.7 + - - +
162A LEU* 5.5 5.3 - - - +
171A SER* 5.4 0.7 - - - -
172A ASN* 1.3 78.1 - - - +
174A ALA* 1.3 61.5 + - - +
141B THR* 6.3 0.7 - - - -
192B ARG* 3.0 33.8 + - - +
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Residues in contact with ALA 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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136A LEU* 3.6 7.2 - - - +
137A PHE* 2.9 31.2 + - + +
140A PHE* 4.8 0.7 - - + -
146A VAL* 3.8 37.5 - - + -
156A ILE* 5.0 0.2 - - + -
157A THR* 3.9 9.0 - - - +
158A ASP 4.2 2.2 - - - +
159A LYS* 4.4 0.2 - - - -
173A SER* 1.3 76.4 - - - +
175A VAL* 1.3 64.9 + - - +
189A PHE* 3.8 13.0 - - + -
192B ARG* 3.6 6.7 - - - +
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Residues in contact with VAL 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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134A VAL* 4.5 8.3 - - + -
135A CYS 3.4 9.4 - - - +
136A LEU* 3.9 14.8 - - + -
155A TYR 3.9 0.3 - - - +
156A ILE* 3.4 2.3 - - - +
157A THR* 2.9 41.7 + - + +
174A ALA* 1.3 80.1 - - - +
176A ALA* 1.3 65.7 + - - +
177A TRP* 4.1 17.5 - - + -
189A PHE* 4.0 1.3 - - - -
143B VAL* 4.2 25.6 - - + -
145B LEU* 5.2 1.3 - - + -
190B SER* 4.0 18.4 - - - +
192B ARG* 3.9 22.9 - - + +
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Residues in contact with ALA 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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134A VAL* 3.6 2.9 - - - +
135A CYS* 2.8 36.4 + - + +
154A VAL* 5.3 0.2 - - + -
155A TYR 3.0 13.2 - - - +
156A ILE* 4.1 5.2 - - + -
175A VAL* 1.3 74.9 - - - +
177A TRP* 1.3 67.0 + - - +
183A PHE* 5.0 0.9 - - + -
188A ALA* 3.7 23.6 - - + -
189A PHE* 3.6 25.5 - - + -
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Residues in contact with TRP 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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132A LYS* 3.9 22.2 - - - +
133A SER 4.2 4.5 - - - +
134A VAL* 4.1 12.8 - - + +
154A VAL* 3.8 1.9 - - - +
155A TYR* 3.0 77.4 + + + -
157A THR* 3.8 25.6 - - + -
175A VAL* 4.1 11.2 - - + -
176A ALA* 1.3 82.2 - - - +
178A SER* 1.3 68.8 + - - +
179A ASN* 4.4 6.8 + - - -
183A PHE* 4.2 10.7 - - - -
145B LEU* 3.8 34.6 - - + +
147B THR* 4.3 9.4 - - + +
176B LEU* 4.2 10.5 - - + -
178B GLU* 5.4 2.1 + - + -
188B ALA* 3.5 34.3 - - + -
189B LEU* 5.2 0.7 - - - -
190B SER* 5.6 0.2 - - - -
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Residues in contact with SER 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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132A LYS* 3.3 15.2 + - - +
133A SER 5.2 1.1 + - - +
153A ASP* 2.5 26.0 + - - +
154A VAL* 4.3 1.3 - - - -
155A TYR* 4.7 1.3 - - - -
177A TRP* 1.3 84.2 - - - +
179A ASN* 1.3 69.6 + - - +
180A LYS* 3.2 26.4 + - - +
183A PHE* 3.7 36.9 - - - -
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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