Contacts of the strand formed by residues 129 - 143 (chain B) in PDB entry 2Z9I
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 129 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A SER* 3.9 7.6 - - - -
140A ARG* 3.3 8.3 + - - +
159A GLN* 3.1 27.0 + - - +
204A LEU* 4.1 3.1 - - + -
119B ALA 3.5 1.7 - - - +
120B ILE* 3.2 6.4 - - - -
121B GLY 2.9 30.8 + - - -
123B PRO* 3.6 19.7 - - + +
126B LEU* 2.7 26.9 + - - +
127B GLU 3.2 0.8 + - - -
128B GLY* 1.3 74.9 - - - +
130B VAL* 1.3 61.1 + - - +
131B THR* 3.8 24.9 - - + -
168B ASN* 5.2 1.2 - - - +
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 3.7 19.7 - - + -
134A ILE* 3.3 21.5 - - + +
136A SER* 2.7 41.1 + - - +
12B ALA* 4.3 8.7 - - + -
16B VAL* 3.5 31.6 - - + -
118B LEU* 4.0 27.6 - - + -
119B ALA 3.4 7.2 - - - +
120B ILE* 4.2 9.9 - - + -
128B GLY 3.8 4.3 - - - +
129B THR* 1.3 75.8 - - - +
131B THR* 1.3 60.6 + - - +
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Residues in contact with THR 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ILE* 4.1 0.4 - - - -
136A SER* 4.1 2.2 - - - +
161A ASP* 3.0 24.9 - - - +
203A GLY 4.4 4.9 - - - +
204A LEU* 5.2 1.8 - - + -
118B LEU* 3.2 5.7 - - - +
119B ALA* 2.8 48.6 + - - +
129B THR* 3.8 20.6 - - + +
130B VAL* 1.3 79.2 - - - +
132B THR* 1.3 64.9 + - - +
162B ALA* 4.1 0.6 - - - +
163B ALA* 2.8 42.0 + - + +
168B ASN* 5.6 0.7 + - - +
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Residues in contact with THR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLY* 5.1 3.6 - - - -
134A ILE* 3.5 36.1 + - + +
161A ASP* 2.8 21.2 + - - +
8B VAL* 4.0 8.3 - - + -
117B VAL 3.5 3.6 - - - -
118B LEU* 2.7 33.2 - - + -
131B THR* 1.3 73.0 - - - +
133B GLY* 1.3 59.7 + - - +
161B ASP 4.2 2.3 - - - +
162B ALA* 3.3 14.9 - - - -
163B ALA 4.4 0.9 + - - -
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Residues in contact with GLY 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B PRO* 3.5 3.5 - - - +
117B VAL* 2.9 31.6 + - - +
132B THR* 1.3 76.7 - - - +
134B ILE* 1.3 70.1 + - - +
161B ASP* 3.4 12.8 - - - -
162B ALA* 3.6 8.7 - - - +
132C THR* 4.4 7.6 - - - -
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Residues in contact with ILE 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B GLY* 3.6 26.0 - - - +
115B GLN 3.2 8.5 - - - +
116B PRO* 4.4 4.5 - - + -
117B VAL* 3.8 7.1 - - - +
133B GLY* 1.3 78.6 - - - +
135B VAL* 1.3 69.4 + - - +
136B SER 3.1 4.2 + - - -
160B THR* 2.9 21.5 + - - -
161B ASP* 2.8 20.6 + - - +
8C VAL* 4.3 10.8 - - + -
118C LEU* 4.7 0.2 - - + -
130C VAL* 3.4 46.7 - - + +
132C THR* 3.7 32.3 - - + +
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU* 3.8 24.2 - - + -
112B ARG 3.4 23.8 - - - +
113B VAL* 3.6 6.4 - - - +
114B GLY* 2.8 28.1 + - - +
115B GLN* 2.9 21.1 + - + +
117B VAL* 4.0 16.4 - - + -
134B ILE* 1.3 74.6 - - - +
136B SER* 1.3 58.3 + - - +
137B ALA 3.6 12.8 - - - +
138B LEU* 3.6 32.3 - - + -
158B ILE* 4.3 6.5 - - + -
159B GLN 3.5 6.1 - - - +
160B THR* 4.7 1.1 - - - +
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Residues in contact with SER 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 3.9 6.0 - - - +
134B ILE 3.1 3.5 + - - -
135B VAL* 1.3 71.9 - - - +
137B ALA* 1.3 59.9 + - - +
159B GLN* 2.7 38.1 + - - -
160B THR* 3.8 0.6 - - - -
161B ASP* 3.5 27.2 + - - +
203B GLY 4.9 0.6 + - - -
128C GLY 3.5 5.7 - - - +
129C THR* 3.9 4.2 - - - -
130C VAL* 2.7 47.8 + - - +
131C THR* 4.0 2.1 - - - +
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B VAL* 3.9 10.1 - - - -
135B VAL* 3.5 8.3 - - - +
136B SER* 1.3 80.0 - - - +
138B LEU* 1.3 69.0 + - - +
140B ARG* 3.4 36.1 - - + +
159B GLN* 3.0 35.3 + - + +
127C GLU 5.3 0.2 - - - +
128C GLY 4.4 4.9 - - - +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B SER 5.7 1.6 - - - +
111B LEU* 3.3 50.5 - - + +
112B ARG* 4.2 9.2 - - - +
113B VAL* 4.2 12.1 - - + +
135B VAL* 3.6 24.0 - - + -
137B ALA* 1.3 80.0 - - - +
139B ASN* 1.3 83.2 + - - +
140B ARG* 3.2 5.3 + - - -
157B ALA 4.1 1.3 - - - -
158B ILE* 4.0 13.7 - - + -
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Residues in contact with ASN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 1.3 84.1 - - - +
140B ARG* 1.3 62.2 + - - +
141B PRO* 3.5 9.5 - - - +
156B ASP* 3.1 39.1 + - - +
157B ALA 3.1 9.6 + - - -
209B PRO* 5.7 2.8 - - - +
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Residues in contact with ARG 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ALA* 3.4 19.0 - - + +
138B LEU 3.2 4.4 - - - +
139B ASN* 1.3 75.9 - - - +
141B PRO* 1.4 80.3 - - + +
142B VAL* 3.4 2.0 + - + -
155B LEU 3.3 0.9 - - - +
156B ASP 4.5 0.2 - - - -
157B ALA* 2.7 48.6 + - + +
159B GLN* 2.8 31.8 - - + +
206B PHE* 3.9 22.0 - - + -
125C GLY 5.2 0.4 + - - -
126C LEU* 3.7 23.7 - - + +
127C GLU* 2.9 40.6 + - - +
129C THR* 3.1 17.8 + - - +
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Residues in contact with PRO 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ASN 3.5 8.5 - - - +
140B ARG* 1.4 93.5 - - + +
142B VAL* 1.3 62.9 + - - +
143B SER 4.3 0.2 - - - -
154B VAL* 4.8 0.7 - - + -
155B LEU 3.3 7.4 - - - +
276B SER* 5.4 1.8 - - - +
278B ASP* 3.9 20.4 - - + +
279B ALA* 3.8 24.9 - - + +
282B ALA* 3.7 20.9 - - + -
126C LEU* 5.8 1.0 - - - +
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ARG* 3.7 11.4 - - + +
141B PRO* 1.3 79.1 - - - +
143B SER* 1.3 61.0 + - - +
144B THR 4.4 0.2 - - - +
153B THR 3.4 1.7 - - - +
154B VAL* 3.1 8.1 - - - +
155B LEU* 2.7 61.9 + - + +
157B ALA* 3.9 2.2 - - + -
206B PHE* 3.6 38.8 - - + -
278B ASP* 6.4 0.2 - - - -
126C LEU* 5.9 0.7 - - + -
408E VAL* 3.2 43.1 - - + -
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Residues in contact with SER 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B PRO 4.3 0.4 - - - -
142B VAL* 1.3 71.2 - - - +
144B THR* 1.3 65.9 + - - +
152B ASN* 4.9 2.9 - - - -
153B THR 3.3 5.8 - - - -
154B VAL* 4.3 10.3 - - - -
278B ASP* 5.9 4.5 + - - +
408E VAL 2.5 34.9 + - - +
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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