Contacts of the strand formed by residues 141 - 155 (chain A) in PDB entry 4PH8
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 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A ASP* 3.3 10.9 - - - -
138A ASN* 2.9 38.7 + - - +
139A LYS 3.3 2.0 + - - -
140A GLN* 1.3 77.4 - - - +
142A GLY* 1.3 68.0 + - - -
143A ALA 3.5 0.2 + - - -
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Residues in contact with GLY 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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136A PHE 3.7 0.7 - - - -
137A ASP* 3.6 16.1 + - - -
138A ASN* 5.0 0.2 - - - +
140A GLN* 4.1 4.6 + - - +
141A GLY* 1.3 73.0 - - - -
143A ALA* 1.3 59.8 + - - +
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Residues in contact with ALA 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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13A ASP* 5.7 0.2 - - - -
135A ASP* 3.5 4.3 - - - +
136A PHE* 2.9 46.6 + - + +
138A ASN* 3.7 30.3 - - - +
140A GLN* 5.8 1.3 - - + -
141A GLY 4.1 0.7 - - - +
142A GLY* 1.3 75.1 - - - +
144A SER* 1.3 63.7 + - - +
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Residues in contact with SER 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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133A ALA* 5.1 5.2 - - - -
134A VAL 3.1 7.6 - - - -
135A ASP* 3.2 26.5 - - - -
136A PHE* 3.9 3.1 - - - -
143A ALA* 1.3 75.2 - - - +
145A GLN* 1.3 75.6 + - - +
146A GLN* 5.9 0.2 - - - +
83B ASP* 3.5 2.3 - - - +
84B GLY* 3.1 44.4 + - - +
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Residues in contact with GLN 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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13A ASP* 4.3 19.0 - - + +
14A CYS 3.6 25.2 + - - +
16A VAL* 3.7 11.5 - - + +
133A ALA* 3.1 4.3 - - - +
134A VAL* 2.9 34.7 + - + -
136A PHE* 3.9 14.3 - - + -
144A SER* 1.3 85.1 - - - +
146A GLN* 1.3 61.1 + - - +
81B SER* 3.8 20.3 + - - -
82B ILE 3.3 4.2 - - - -
83B ASP* 3.6 17.3 + - - +
109B ASN* 4.8 5.0 - - - +
110B ALA* 5.3 1.2 - - - +
111B SER* 3.4 26.1 + - - +
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Residues in contact with GLN 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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16A VAL* 3.9 3.1 - - - -
56A TRP* 3.8 22.7 - - + -
131A HIS* 4.6 7.4 + - - -
132A ALA 3.1 12.6 - - - +
133A ALA* 3.8 9.6 - - + -
145A GLN* 1.3 75.4 - - - +
147A THR* 1.3 62.9 + - - +
81B SER* 3.2 4.9 - - - -
82B ILE* 2.8 51.4 + - + +
83B ASP 3.1 14.9 + - - -
84B GLY* 3.6 15.5 + - - -
86B ALA 2.9 27.6 + - - -
87B ASP* 5.4 1.5 + - - +
88B PHE* 4.0 4.8 - - + -
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Residues in contact with THR 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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16A VAL* 3.9 25.6 - - + +
18A ILE* 3.7 28.3 - - + -
131A HIS* 3.5 7.8 + - - +
132A ALA* 2.9 28.5 + - + +
146A GLN* 1.3 77.6 - - - +
148A THR* 1.3 67.6 + - - +
79B ASN* 3.1 22.3 + - - +
80B PRO 3.1 12.3 + - - -
81B SER* 3.8 11.6 + - - -
88B PHE* 3.8 10.7 - - - -
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Residues in contact with THR 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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18A ILE* 4.9 1.3 - - - +
129A ILE* 3.4 21.1 - - - +
130A LEU 2.9 18.2 + - - -
131A HIS* 4.2 6.9 + - - -
132A ALA 4.9 0.4 - - - +
147A THR* 1.3 83.0 + - - +
149A GLN* 1.3 61.7 + - - +
79B ASN* 2.8 32.5 + - - +
88B PHE* 4.0 32.8 - - + -
92B GLY* 3.8 20.0 + - - +
94B ASP 5.1 1.8 - - - +
95B ALA* 5.7 2.2 - - - -
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Residues in contact with GLN 149 (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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18A ILE* 3.6 31.7 + - + +
19A THR* 4.1 4.6 - - - +
20A THR* 3.3 48.6 + - + +
128A MET 3.8 0.5 - - - +
129A ILE* 3.8 0.3 - - - -
130A LEU* 2.9 34.6 + - - +
148A THR* 1.3 78.5 + - - +
150A THR* 1.3 68.7 + - - +
151A ILE* 4.0 0.7 + - - +
201A GOL 3.8 26.1 + - - +
79B ASN* 5.0 4.9 + - - +
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Residues in contact with THR 150 (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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20A THR* 4.7 2.3 + - - -
127A THR* 3.6 32.5 - - + -
128A MET 3.4 7.2 - - - +
129A ILE* 4.0 17.2 - - + +
148A THR* 5.8 0.3 - - - +
149A GLN* 1.3 80.3 + - - +
151A ILE* 1.3 66.2 + - - +
152A ARG* 3.9 29.4 + - - +
201A GOL 3.9 21.6 + - - -
92B GLY 4.1 11.4 + - - -
93B THR* 4.9 4.9 + - + -
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Residues in contact with ILE 151 (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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20A THR* 3.5 36.3 - - + +
21A THR* 4.6 11.4 - - - +
22A PRO 5.6 0.7 - - - +
36A PHE* 3.5 39.3 - - + -
37A SER 4.0 11.2 - - - +
64A TRP* 5.1 0.7 - - + -
66A LEU* 5.0 1.2 - - + +
127A THR* 3.2 5.9 - - - -
128A MET* 2.7 62.7 + - + +
130A LEU* 3.6 28.9 - - + -
149A GLN 5.2 0.2 - - - +
150A THR* 1.3 74.0 - - - +
152A ARG* 1.3 66.0 + - - +
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Residues in contact with ARG 152 (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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21A THR 5.4 0.8 + - - -
22A PRO 4.4 1.0 - - - +
23A PRO* 3.5 28.5 - - + +
24A GLN 3.2 20.0 + - - -
36A PHE* 4.4 3.9 - - - -
66A LEU* 5.5 0.4 - - - -
125A GLU* 6.0 1.6 - - - +
126A TYR 3.5 3.1 - - - +
127A THR* 3.3 27.8 - - + +
150A THR* 3.9 17.1 + - + +
151A ILE* 1.3 87.3 - - - +
153A LEU* 1.3 63.0 + - - +
154A THR* 5.9 1.3 - - - +
201A GOL 2.2 44.1 + - - -
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Residues in contact with LEU 153 (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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24A GLN* 3.4 31.6 - - + +
26A VAL* 4.3 12.1 - - + +
34A ILE* 4.2 28.9 - - + -
36A PHE* 4.0 17.5 - - + -
66A LEU* 4.0 23.3 - - + +
114A VAL* 5.8 0.7 - - + -
121A LEU* 5.1 4.5 - - + -
124A GLY 4.0 0.5 - - - +
125A GLU* 3.7 2.8 - - - +
126A TYR* 2.8 51.3 + - + +
152A ARG* 1.3 75.1 - - - +
154A THR* 1.3 71.3 + - - +
155A VAL* 4.0 17.9 - - + -
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Residues in contact with THR 154 (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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24A GLN 2.8 9.0 + - - +
25A THR* 3.2 26.2 - - + +
26A VAL* 2.9 26.2 + - - +
124A GLY 3.6 5.8 - - - +
125A GLU* 2.6 34.5 + - - +
152A ARG* 5.9 1.4 - - - +
153A LEU* 1.3 74.2 - - - +
155A VAL* 1.3 64.4 + - - +
156A THR 3.7 18.4 - - - +
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Residues in contact with VAL 155 (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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26A VAL* 3.3 7.4 - - + +
28A VAL* 3.9 17.3 - - + -
121A LEU* 4.0 20.0 - - + -
122A ILE 3.3 32.1 - - - +
123A PRO* 3.6 10.0 - - + +
124A GLY* 2.9 27.3 + - - +
126A TYR* 3.6 21.5 - - + -
153A LEU* 4.0 16.2 - - + -
154A THR* 1.3 75.1 - - - +
156A THR* 1.3 79.4 + - - +
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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