Contacts of the strand formed by residues 128 - 138 (chain A) in PDB entry 1ZA3
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 THR 128 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A GLN* 2.9 45.1 - - + +
124A LEU* 3.7 4.3 + - - -
126A SER* 4.3 7.7 + - - -
127A GLY* 1.3 82.3 + - - +
129A ALA* 1.3 65.7 + - - +
130A SER* 4.4 2.2 - - - +
179A THR* 4.5 6.5 - - - +
180A LEU 3.7 10.6 + - - +
181A SER* 4.6 2.6 - - - +
182A LYS* 4.1 5.7 - - - +
143B LYS* 4.2 23.1 - - + +
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Residues in contact with ALA 129 (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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119A PRO* 4.2 5.6 - - + -
123A GLN* 3.9 1.1 - - - +
124A LEU* 3.3 27.4 - - + -
128A THR* 1.3 75.4 - - - +
130A SER* 1.3 60.6 + - - +
131A VAL* 4.0 3.3 + - - +
178A LEU 3.6 1.7 - - - +
179A THR* 3.5 3.1 - - - -
180A LEU* 2.8 40.0 + - + +
182A LYS* 4.8 1.8 - - - -
185A TYR* 3.9 27.8 - - + -
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Residues in contact with SER 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PHE 4.1 1.0 - - - +
118A PRO 4.3 0.7 - - - +
119A PRO* 3.5 20.6 - - - +
123A GLN* 2.6 33.3 + - - +
128A THR* 4.4 0.2 - - - +
129A ALA* 1.3 70.3 - - - +
131A VAL* 1.3 62.7 + - - +
132A VAL* 3.9 6.0 + - - +
177A THR* 4.4 10.4 - - - +
178A LEU 3.4 6.7 - - - -
179A THR* 3.9 7.8 + - - -
124B LEU* 5.3 2.8 - - - +
141B LEU* 3.5 21.5 - - - +
143B LYS* 3.5 19.1 - - - -
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 4.2 3.6 - - + -
117A PHE 3.3 17.9 - - - +
119A PRO* 4.2 15.7 - - + -
129A ALA 4.9 3.4 - - - +
130A SER* 1.3 74.3 - - - +
132A VAL* 1.3 59.9 + - - +
147A TRP* 3.7 26.0 - - + -
176A SER 3.7 1.0 - - - +
177A THR* 3.5 1.9 - - - -
178A LEU* 2.9 51.8 + - + +
180A LEU* 5.8 2.2 - - + -
185A TYR* 4.7 4.9 - - + -
191A TYR* 4.4 13.7 - - + -
208A PHE* 3.4 26.2 - - + -
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 3.6 2.8 - - - +
117A PHE* 2.8 54.1 + - + +
130A SER 4.3 6.5 - - - +
131A VAL* 1.3 76.9 - - - +
133A CYS* 1.3 69.6 + - - +
134A LEU* 5.1 3.1 - - + -
147A TRP* 4.3 1.6 - - - -
175A SER* 4.6 11.9 - - - -
176A SER 3.5 6.7 - - - +
177A THR* 3.8 26.2 - - + +
124B LEU* 4.2 27.4 - - + -
141B LEU* 4.8 6.7 - - + -
179B SER* 4.5 11.7 - - - +
181B VAL* 5.9 2.2 - - + -
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Residues in contact with CYS 133 (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 VAL* 4.1 3.8 - - - -
115A PHE 3.3 6.7 - - - -
116A ILE* 5.0 0.2 - - + -
132A VAL* 1.3 76.6 - - - +
134A LEU* 1.3 63.6 + - - +
135A LEU* 4.0 18.6 - - - +
145A VAL* 4.3 5.8 - - - -
147A TRP* 3.6 19.1 - - + -
174A LEU 3.5 2.1 - - - +
175A SER* 3.4 3.1 - - - -
176A SER* 2.8 39.5 + - - +
193A CYS* 2.1 46.9 - - + -
195A VAL* 4.5 0.4 - - - -
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Residues in contact with LEU 134 (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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113A SER 3.2 5.0 - - - +
114A VAL* 3.3 1.9 - - - -
115A PHE* 2.9 44.3 + - + +
117A PHE* 3.7 22.7 - - + -
132A VAL* 5.1 3.4 - - + -
133A CYS* 1.3 76.4 - - - +
135A LEU* 1.3 76.9 + - - +
136A ASN* 4.1 11.2 - - + +
173A SER* 5.0 0.2 - - - -
174A LEU 3.5 2.0 - - - -
175A SER* 4.6 1.8 - - - +
137B ALA* 4.1 19.1 - - + -
166B PHE* 3.9 25.8 - - + -
181B VAL* 3.7 38.8 - - + -
183B THR* 5.9 0.4 - - + -
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Residues in contact with LEU 135 (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* 3.8 19.7 - - + -
113A SER 3.3 3.8 - - - -
114A VAL* 4.4 2.5 - - + -
133A CYS* 4.0 14.6 - - - +
134A LEU* 1.3 81.3 - - - +
136A ASN* 1.3 60.1 + - - +
138A PHE* 3.8 17.5 - - + -
143A ALA* 4.2 16.4 - - + -
145A VAL* 3.9 21.3 - - + -
173A SER* 3.2 8.7 - - - -
174A LEU* 2.9 43.9 + - + +
195A VAL* 3.5 45.8 - - + -
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Residues in contact with ASN 136 (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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111A ALA 4.4 0.5 - - - +
112A PRO* 3.9 1.6 - - - +
113A SER* 2.9 45.1 + - - +
115A PHE* 4.4 7.4 - - + -
134A LEU* 4.1 14.4 - - + +
135A LEU* 1.3 73.8 - - - +
137A ASN* 1.3 95.4 + - - +
138A PHE 3.7 1.1 - - - -
173A SER* 4.2 0.4 - - - -
162B GLY 5.2 1.5 + - - +
164B HIS* 3.2 25.7 + - - -
181B VAL* 4.7 3.1 - - - +
183B THR* 3.2 33.2 + - - +
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Residues in contact with ASN 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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110A ALA* 4.1 5.2 - - - +
111A ALA 3.8 7.8 - - - +
136A ASN* 1.3 97.8 - - - +
138A PHE* 1.3 57.6 + - - +
166A ASP* 5.4 2.3 - - - +
169A ASP* 4.4 9.0 - - - +
171A THR* 3.5 31.1 + - + +
172A TYR 3.2 14.1 + - - -
173A SER* 3.4 3.8 + - - -
162B GLY* 5.9 2.2 + - - -
164B HIS* 3.2 26.2 + - - -
183B THR* 5.0 3.6 + - - -
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Residues in contact with PHE 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ALA* 3.3 16.4 - - - +
112A PRO* 3.6 33.0 - - + -
135A LEU* 3.8 21.8 - - + -
137A ASN* 1.3 74.9 - - - +
139A TYR* 1.3 60.9 + - - +
140A PRO 3.1 28.7 - - - -
141A ARG* 3.4 21.5 - - - -
142A GLU 4.3 1.6 - - - -
143A ALA* 4.4 11.2 - - + -
162A VAL* 5.1 1.1 - - + -
171A THR* 3.3 7.1 - - - -
172A TYR* 2.7 68.6 + - + -
173A SER* 3.7 14.1 - - - -
174A LEU* 3.8 15.9 - - + -
197A HIS* 3.7 15.0 - + - -
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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