Contacts of the strand formed by residues 136 - 148 (chain A) in PDB entry 2ZDZ
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 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A PRO* 3.7 1.9 - - - +
133A TYR* 2.9 35.4 + - - +
135A GLN* 1.3 84.5 - - - +
137A LYS* 1.3 68.0 + - - +
168A ASP* 3.3 21.8 - - - -
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Residues in contact with LYS 137 (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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130A TYR* 3.6 31.3 + - + +
131A VAL 3.2 15.9 - - - +
132A PRO* 3.9 9.0 - - + -
133A TYR* 3.4 11.3 + - - -
136A GLY* 1.3 78.6 - - - +
138A TRP* 1.3 66.3 + - - +
139A GLU* 4.8 8.3 - - + +
166A GLU* 5.1 1.8 - - + +
167A SER* 3.2 7.8 - - - +
168A ASP* 2.7 63.2 + - - +
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Residues in contact with TRP 138 (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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1A 310 3.5 44.0 - + + +
99A ASN* 4.3 16.6 - - + -
101A ALA* 3.9 18.2 - - + -
129A VAL* 3.8 18.2 - - + -
130A TYR* 3.9 1.0 - - - -
131A VAL* 2.9 69.2 + - + +
133A TYR* 4.1 2.0 - + - -
137A LYS* 1.3 77.4 - - - +
139A GLU* 1.3 66.5 + - - +
140A GLY 4.9 0.7 - - - -
162A ALA* 3.7 26.2 - - + -
164A ILE* 3.8 26.0 - - + -
166A GLU 3.6 4.7 - - - -
167A SER* 4.0 11.7 - - - -
170A PHE* 3.5 31.2 - + + -
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Residues in contact with GLU 139 (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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129A VAL 3.4 12.1 - - - +
130A TYR* 3.3 34.5 - - + +
137A LYS* 4.8 7.3 - - + +
138A TRP* 1.3 78.7 - - - +
140A GLY* 1.3 62.0 + - - +
164A ILE* 3.4 4.9 - - - -
165A THR* 2.9 24.8 + - - +
166A GLU* 2.8 37.8 + - + +
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Residues in contact with GLY 140 (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 GLY* 3.4 4.3 - - - -
129A VAL* 2.8 43.1 + - - +
138A TRP* 5.2 1.6 - - - -
139A GLU* 1.3 78.8 - - - +
141A GLU* 1.3 66.4 + - - +
163A ALA 3.1 16.8 - - - -
164A ILE* 4.2 0.4 - - - -
165A THR* 3.9 6.5 - - - -
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Residues in contact with GLU 141 (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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116A ARG* 2.7 45.3 + - - +
122A TYR* 4.9 1.6 + - - +
124A ASP* 5.3 4.0 - - - +
127A LYS 3.7 7.4 - - - +
128A GLY* 5.1 3.4 - - - -
140A GLY* 1.3 77.0 - - - +
142A LEU* 1.3 66.1 + - - +
161A ILE 3.6 1.0 - - - +
163A ALA* 2.9 33.7 + - - +
165A THR* 4.0 18.0 + - - +
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Residues in contact with LEU 142 (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 TYR* 3.8 2.8 + - - -
124A ASP* 3.2 10.6 - - - +
125A LEU* 3.1 34.0 + - + +
126A ARG 4.2 0.2 + - - -
127A LYS* 2.8 51.4 + - + +
128A GLY 4.3 3.1 - - - +
129A VAL* 3.9 26.7 - - + -
141A GLU* 1.3 73.3 - - - +
143A GLY* 1.3 57.2 + - - +
160A ASN* 6.1 0.2 - - + -
161A ILE 3.6 4.3 - - - +
162A ALA* 4.0 16.8 - - + +
190A ARG 4.9 0.2 - - - +
191A PRO* 4.0 19.3 - - + -
195A LEU* 3.9 33.2 - - + -
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Residues in contact with GLY 143 (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 TYR* 4.0 13.9 + - - -
123A ARG 3.2 12.6 - - - -
125A LEU* 3.8 11.0 - - - +
141A GLU 3.9 0.2 + - - -
142A LEU* 1.3 77.0 - - - +
144A THR* 1.3 61.4 + - - +
160A ASN* 3.4 5.2 - - - -
161A ILE* 2.7 37.5 + - - -
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Residues in contact with THR 144 (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 TYR* 3.4 5.1 - - - -
123A ARG* 2.9 43.8 + - - +
125A LEU* 4.2 15.9 - - + -
143A GLY* 1.3 75.0 - - - -
145A ASP* 1.3 65.6 + - - +
158A ARG* 2.8 36.3 + - + -
159A ALA 3.2 13.5 - - - +
160A ASN* 3.4 25.1 - - - +
161A ILE* 4.4 2.5 - - - +
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Residues in contact with ASP 145 (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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82A VAL* 4.2 2.2 - - + -
83A GLY* 3.4 11.3 - - - -
114A TYR* 2.6 28.2 + - - +
119A SER* 2.7 24.2 + - - -
121A THR* 2.7 30.1 + - - -
122A TYR* 3.6 10.1 - - - +
144A THR* 1.3 76.8 - - - +
146A LEU* 1.3 74.8 + - - +
147A VAL* 3.7 4.2 + - - +
158A ARG* 3.4 12.2 - - - +
159A ALA 3.0 28.9 + - - +
161A ILE* 3.5 12.0 - - + +
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Residues in contact with LEU 146 (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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81A THR 3.9 0.3 - - - +
82A VAL* 3.5 3.6 - - - +
83A GLY 2.8 33.0 + - - +
84A SER* 3.7 20.6 - - - +
121A THR* 3.8 22.4 - - + +
145A ASP* 1.3 80.5 + - - +
147A VAL* 1.3 60.5 + - - +
156A THR* 3.8 21.1 - - + -
157A VAL 3.4 2.5 - - - +
158A ARG* 3.7 38.4 - - + +
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Residues in contact with VAL 147 (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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80A MET* 3.5 32.1 - - + -
81A THR 3.3 11.0 - - - +
82A VAL* 4.3 4.0 - - + -
100A PHE* 3.9 26.2 - - + -
145A ASP 3.7 11.2 - - - +
146A LEU* 1.3 81.0 - - - +
148A SER* 1.3 67.8 + - - +
155A VAL 4.3 0.3 - - - +
156A THR* 3.5 1.4 - - - +
157A VAL* 2.7 36.3 + - - +
159A ALA* 4.1 10.5 - - + -
161A ILE* 4.1 11.0 - - + -
198A PHE* 3.8 17.2 - - + -
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Residues in contact with SER 148 (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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80A MET* 3.3 8.8 - - - +
81A THR* 2.9 44.1 + - - -
147A VAL* 1.3 75.8 + - - +
149A ILE* 1.3 68.3 + - - +
150A PRO* 3.8 2.7 - - - -
155A VAL 3.9 10.8 - - - -
156A THR* 2.9 30.3 + - - +
198A PHE* 6.1 0.7 - - - -
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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