Contacts of the strand formed by residues 129 - 143 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ALA 3.5 1.7 - - - +
120A ILE* 3.3 5.4 - - - -
121A GLY 2.9 33.8 + - - -
123A PRO* 3.6 19.4 - - + +
126A LEU* 2.8 26.0 + - - +
127A GLU 3.3 0.6 - - - -
128A GLY* 1.3 74.5 - - - +
130A VAL* 1.3 61.4 + - - +
131A THR* 4.0 23.6 - - + -
168A ASN* 5.2 1.9 - - - +
136C SER* 3.7 8.1 - - - -
140C ARG* 3.1 9.1 + - - +
159C GLN* 2.9 28.6 + - - +
204C LEU* 4.1 3.1 - - + -
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ALA* 4.4 8.3 - - + -
16A VAL* 3.6 30.7 - - + -
118A LEU* 3.9 27.6 - - + -
119A ALA 3.4 6.7 - - - +
120A ILE* 4.1 9.6 - - + -
128A GLY 3.8 3.1 - - - +
129A THR* 1.3 76.1 - - - +
131A THR* 1.3 62.7 + - - +
113C VAL* 3.7 18.6 - - + -
114C GLY* 5.2 0.2 - - - -
134C ILE* 3.4 23.0 - - + +
136C SER* 2.6 43.4 + - - +
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Residues in contact with THR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 3.2 7.3 - - - +
119A ALA* 2.9 44.8 + - - +
123A PRO* 6.2 0.2 - - + -
129A THR* 4.0 18.4 + - + +
130A VAL* 1.3 77.9 - - - +
132A THR* 1.3 61.5 + - - +
162A ALA* 4.2 1.1 - - - -
163A ALA* 2.8 44.3 + - + +
168A ASN* 5.4 1.4 + - - +
134C ILE* 4.4 2.9 - - - -
136C SER* 4.1 0.9 - - - +
161C ASP* 2.8 26.5 - - - +
203C GLY 4.4 4.5 - - - +
204C LEU* 5.3 2.0 - - + -
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Residues in contact with THR 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.5 8.7 - - - +
116A PRO* 6.0 1.6 - - - +
117A VAL 3.6 3.9 + - - -
118A LEU* 3.1 22.4 - - - +
131A THR* 1.3 74.8 - - - +
133A GLY* 1.3 62.2 + - - +
161A ASP* 4.4 2.1 - - - +
162A ALA* 3.4 14.3 - - - -
163A ALA 4.5 0.5 + - - -
176A MSE 5.3 0.9 - - - +
133C GLY* 5.3 4.3 - - - -
134C ILE* 4.0 29.7 - - + +
161C ASP* 2.8 18.8 + - + +
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Residues in contact with GLY 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PRO* 3.3 7.6 - - - +
117A VAL* 2.9 31.5 + - - +
132A THR* 1.3 80.6 + - - +
134A ILE* 1.3 67.5 + - - +
161A ASP* 3.9 6.7 - - - -
162A ALA* 3.8 15.0 - - - +
132B THR* 5.2 2.9 - - - -
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Residues in contact with ILE 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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114A GLY* 3.6 25.6 - - - +
115A GLN 3.1 10.8 - - - +
116A PRO* 4.2 4.5 - - + -
117A VAL* 3.8 4.0 - - - -
133A GLY* 1.3 80.1 - - - +
135A VAL* 1.3 71.5 + - - +
136A SER 3.3 3.8 + - - -
160A THR* 2.7 26.4 + - - -
161A ASP* 3.4 20.6 + - + +
8B VAL* 4.5 4.0 - - + -
130B VAL* 3.3 42.6 - - + +
131B THR* 4.1 0.7 - - - -
132B THR* 3.5 37.0 - - + +
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 4.1 20.9 - - + -
112A ARG 3.4 25.6 - - - +
113A VAL* 3.5 9.9 - - - +
114A GLY 2.8 24.6 + - - -
115A GLN* 2.9 19.1 + - + +
117A VAL* 4.1 16.2 - - + -
134A ILE* 1.3 73.9 - - - +
136A SER* 1.3 62.0 + - - +
137A ALA 3.7 19.5 - - - +
138A LEU* 3.8 20.2 - - + -
158A ILE* 4.3 9.9 - - + -
159A GLN 3.6 6.1 - - - +
160A THR* 4.9 0.7 - - - -
173A LEU* 5.6 0.2 - - + -
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 3.6 10.2 - - - +
134A ILE* 3.3 1.8 + - - +
135A VAL* 1.3 73.2 - - - +
137A ALA* 1.3 62.3 + - - +
159A GLN* 2.8 34.9 + - - -
160A THR* 3.8 0.4 - - - -
161A ASP* 3.3 27.2 + - - -
203A GLY 4.9 0.6 + - - -
128B GLY 3.5 5.4 - - - +
129B THR* 4.2 2.0 - - - -
130B VAL* 2.7 48.2 + - - -
131B THR* 4.1 1.9 - - - +
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Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A VAL* 3.8 9.4 - - - -
135A VAL* 3.5 2.8 - - - +
136A SER* 1.3 81.2 - - - +
138A LEU* 1.3 75.2 + - - +
140A ARG* 3.3 35.0 - - + +
157A ALA 4.8 0.2 - - - -
159A GLN* 3.0 36.6 + - + +
127B GLU 4.9 0.7 - - - +
128B GLY 4.4 5.2 - - - +
129B THR* 4.9 0.2 - - - -
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Residues in contact with LEU 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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108A SER 5.5 1.3 - - - +
111A LEU* 3.3 44.6 - - + +
112A ARG* 4.0 10.3 - - - -
113A VAL* 4.1 12.4 - - + +
135A VAL* 3.8 15.0 - - + -
137A ALA* 1.3 85.3 - - - +
139A ASN* 1.3 83.3 + - - +
140A ARG* 3.3 6.6 + - - +
157A ALA 3.8 1.6 - - - -
158A ILE* 4.1 20.6 - - + -
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Residues in contact with ASN 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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138A LEU* 1.3 84.5 - - - +
140A ARG* 1.3 62.3 + - - +
141A PRO* 3.4 9.5 - - - +
156A ASP* 3.3 23.3 + - - +
157A ALA 3.2 7.9 + - - -
272A ARG* 3.4 50.6 + - + +
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ALA* 3.3 19.1 - - + +
138A LEU 4.1 5.8 - - - +
139A ASN* 1.3 74.0 - - - +
141A PRO* 1.3 77.4 - - + +
142A VAL* 3.3 9.7 + - + -
155A LEU 3.4 0.7 - - - +
156A ASP* 4.6 0.7 - - - -
157A ALA* 2.8 48.6 + - + +
159A GLN* 2.9 32.9 - - + +
206A PHE* 3.9 23.1 - - + -
125B GLY 5.0 0.4 + - - -
126B LEU* 3.5 23.3 + - + +
127B GLU* 2.7 55.3 + - - +
129B THR* 3.3 13.7 + - - +
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Residues in contact with PRO 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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139A ASN 3.4 9.4 - - - +
140A ARG* 1.3 95.0 - - + +
142A VAL* 1.3 61.5 + - - +
143A SER 4.2 0.4 + - - -
154A VAL* 4.7 1.3 - - + -
155A LEU 3.4 8.3 - - - +
272A ARG* 5.9 0.4 - - - +
275A ASN* 5.5 3.4 - - - +
276A SER* 4.9 3.1 - - - +
278A ASP* 3.8 17.3 - - + +
279A ALA* 3.8 38.8 - - + +
282A ALA* 3.9 6.9 - - + -
126B LEU* 5.7 1.6 - - - +
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Residues in contact with VAL 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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140A ARG* 3.7 12.1 - - + +
141A PRO* 1.3 78.1 - - - +
143A SER* 1.3 59.5 + - - +
144A THR 4.0 0.8 + - - +
153A THR 3.5 2.1 - - - +
154A VAL* 3.2 4.7 - - - +
155A LEU* 2.7 59.1 + - + +
157A ALA* 4.0 2.5 - - + -
186A ALA* 4.6 1.1 - - + -
206A PHE* 3.6 44.9 - - + -
126B LEU* 5.7 0.9 - - + -
408D VAL* 3.1 39.7 - - + -
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Residues in contact with SER 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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141A PRO 4.2 0.8 + - - -
142A VAL* 1.3 74.1 - - - +
144A THR* 1.3 60.4 + - - +
152A ASN* 4.1 12.3 - - - -
153A THR 3.3 5.2 - - - -
154A VAL* 3.8 14.6 - - - +
278A ASP* 2.9 27.7 + - - -
408D VAL* 3.5 23.2 - - - +
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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