Contacts of the strand formed by residues 150 - 163 (chain A) in PDB entry 1PU5
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 LYS 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A SER* 3.2 4.8 - - - -
147A SER* 2.9 37.0 + - - +
148A SER* 4.5 9.6 - - - +
149A GLY* 1.3 76.3 - - - +
151A ARG* 1.3 65.8 + - - +
152A LEU* 3.4 10.7 + - + +
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Residues in contact with ARG 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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10A CYS* 4.9 3.0 - - - +
11A ASP* 6.1 1.8 - - - +
15A ASP* 4.0 21.7 + - - +
16A PRO* 4.0 9.4 - - - +
142A GLU* 5.1 2.2 + - - -
144A VAL* 3.6 28.2 - - + +
145A LEU 4.1 7.2 - - - +
146A SER* 4.3 3.8 - - - -
149A GLY 3.5 4.2 + - - +
150A LYS* 1.3 73.1 - - - +
152A LEU* 1.3 66.0 + - - +
153A GLY 4.5 4.9 - - - +
154A CYS* 3.2 38.4 - - - +
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Residues in contact with LEU 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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15A ASP* 3.3 4.5 - - - +
16A PRO* 3.2 27.2 - - + +
17A ALA* 2.9 29.0 + - + -
45A VAL* 4.0 16.4 - - + -
46A PRO 5.4 1.6 - - - +
47A LEU* 4.0 16.8 - - + -
48A SER 6.0 0.4 - - - +
51A LEU* 3.9 17.7 - - + -
145A LEU* 2.8 24.6 + - + +
146A SER* 3.8 9.4 - - - -
147A SER* 3.8 26.5 - - - +
150A LYS* 3.8 15.9 - - + +
151A ARG* 1.3 79.1 - - - +
153A GLY* 1.3 57.3 + - - +
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Residues in contact with GLY 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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15A ASP* 3.9 9.1 - - - +
17A ALA* 3.5 17.7 - - - -
143A SER 4.5 0.2 - - - -
144A VAL* 3.5 4.2 - - - +
145A LEU* 2.8 36.2 + - - +
151A ARG* 3.9 2.3 - - - +
152A LEU* 1.3 79.6 - - - +
154A CYS* 1.3 64.7 - - - +
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Residues in contact with CYS 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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9A ASN* 3.3 5.2 + - - +
10A CYS* 2.1 66.3 + - + -
11A ASP 4.8 0.3 + - - -
15A ASP* 3.9 6.7 + - - +
17A ALA 4.6 1.6 + - - -
142A GLU* 4.1 12.3 - - - -
143A SER 3.2 7.4 - - - +
144A VAL* 3.9 12.3 - - + -
151A ARG* 3.2 33.2 - - - +
153A GLY* 1.3 76.9 - - - +
155A ILE* 1.3 72.2 + - - +
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Residues in contact with ILE 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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7A TRP* 5.3 3.1 - - + -
8A ASP 3.3 10.5 - - - +
9A ASN* 3.5 19.1 - - - +
10A CYS* 3.8 0.9 - - - -
18A VAL* 5.6 0.4 - - - -
19A ILE* 3.6 30.3 - - + -
22A LEU* 5.5 3.6 - - + -
141A ILE* 3.8 1.1 - - + +
142A GLU* 3.3 5.0 - - - +
143A SER* 2.9 47.9 + - - +
154A CYS* 1.3 84.1 - - - +
156A LYS* 1.3 65.3 + - - +
157A ILE* 4.0 27.1 - - + -
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Residues in contact with LYS 156 (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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7A TRP* 3.1 5.7 - - - +
8A ASP* 2.9 39.2 + - + +
9A ASN 6.0 0.2 - - - -
10A CYS* 4.0 22.2 - - - +
141A ILE 3.3 5.8 - - - +
142A GLU* 4.2 22.9 - - + +
155A ILE* 1.3 78.5 - - - +
157A ILE* 1.3 62.6 + - - +
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Residues in contact with ILE 157 (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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5A PHE* 3.5 28.9 - - + -
6A SER 3.4 4.5 - - - +
7A TRP* 4.0 11.9 - - + -
22A LEU* 3.9 17.5 - - + -
24A LEU* 5.1 4.0 - - + -
140A ARG* 3.1 6.3 - - - +
141A ILE* 2.9 52.5 + - + -
155A ILE* 4.0 24.2 - - + -
156A LYS* 1.3 80.0 - - - +
158A ALA* 1.3 68.1 + - - +
159A ALA* 4.6 5.6 - - + +
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Residues in contact with ALA 158 (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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3A SER* 5.7 4.5 - - - +
4A SER 4.3 8.3 - - - +
5A PHE* 3.2 8.3 - - - -
6A SER* 2.8 48.2 + - - +
65A TRP* 6.2 1.6 - - + -
139A TYR 3.5 9.2 - - - +
140A ARG* 4.3 5.6 - - + +
157A ILE* 1.3 74.1 - - - +
159A ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 159 (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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4A SER 4.8 1.1 - - - -
5A PHE* 4.1 20.4 - - + +
24A LEU* 4.3 5.6 - - + -
29A ILE* 4.3 20.6 - - + -
138A ASN* 3.9 0.2 - - - -
139A TYR* 2.8 38.0 + - + +
157A ILE* 4.2 5.8 - - + -
158A ALA* 1.3 76.3 - - - +
160A SER* 1.3 64.9 + - - +
161A LEU* 5.5 2.0 - - + -
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Residues in contact with SER 160 (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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2A MET* 3.9 11.4 - - - -
3A SER* 2.8 27.2 + - - -
4A SER 5.4 0.4 - - - -
27A ASP* 4.7 5.7 + - - -
28A PRO* 3.5 12.7 - - - +
29A ILE* 2.8 27.4 + - - +
137A GLY 3.2 5.8 - - - -
138A ASN* 2.7 30.6 + - - -
159A ALA* 1.3 78.5 - - - +
161A LEU* 1.3 66.6 + - - +
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Residues in contact with LEU 161 (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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2A MET* 2.9 10.6 - - - +
28A PRO* 4.4 0.7 - - - -
29A ILE* 3.3 35.4 - - + +
31A VAL* 4.3 9.2 - - + -
125A VAL* 6.1 2.2 - - + -
128A LEU* 5.5 9.9 - - + -
135A THR* 3.6 31.6 - - + +
136A THR* 3.9 1.1 - - - -
137A GLY 2.8 28.7 + - - -
139A TYR* 3.6 31.2 - - + -
159A ALA* 5.5 2.7 - - + -
160A SER* 1.3 82.4 - - - +
162A LYS* 1.3 62.0 + - - +
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Residues in contact with LYS 162 (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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2A MET* 4.3 4.5 - - + +
28A PRO* 4.0 25.3 - - + +
29A ILE 2.9 8.2 + - - +
30A VAL* 3.3 17.9 - - + +
31A VAL 2.9 24.3 + - - -
135A THR* 4.7 1.6 - - - -
136A THR* 3.7 12.8 - - + +
161A LEU* 1.3 75.1 - - - +
163A GLY* 1.3 76.0 + - - +
164A ILE 4.7 6.3 - - - +
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Residues in contact with GLY 163 (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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31A VAL* 3.0 11.9 - - - -
132A SER* 2.9 24.2 + - - -
135A THR* 4.3 10.6 - - - +
136A THR* 2.9 15.8 + - - -
162A LYS* 1.3 82.2 - - - +
164A ILE* 1.3 75.0 + - - +
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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