Contacts of the strand formed by residues 150 - 163 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B SER* 3.1 5.0 - - - -
147B SER* 2.9 36.1 + - - +
148B SER* 4.1 11.4 - - - +
149B GLY* 1.3 79.4 - - - +
151B ARG* 1.3 64.9 + - - +
152B LEU* 3.3 10.6 + - + +
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Residues in contact with ARG 151 (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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10B CYS* 5.3 2.0 - - - +
11B ASP* 5.2 6.8 + - - +
15B ASP* 3.8 24.1 + - - +
16B PRO* 4.2 9.7 - - - +
142B GLU* 5.3 2.8 + - - -
144B VAL* 3.6 36.1 - - + +
145B LEU 3.9 2.9 - - - +
146B SER* 4.2 3.6 - - - -
149B GLY 3.6 4.2 + - - -
150B LYS* 1.3 71.0 - - - +
152B LEU* 1.3 64.6 + - - +
153B GLY 4.5 3.8 - - - +
154B CYS* 3.7 28.5 - - - +
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Residues in contact with LEU 152 (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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15B ASP* 3.4 4.1 - - - +
16B PRO* 3.3 14.7 - - + +
17B ALA* 3.0 29.6 + - + +
45B VAL* 4.3 20.4 - - + -
46B PRO 5.3 3.1 - - - +
47B LEU* 4.0 17.9 - - + -
48B SER 5.9 0.9 - - - +
51B LEU* 3.8 23.3 - - + -
145B LEU* 2.8 23.9 + - + +
146B SER* 3.9 2.9 - - - -
147B SER* 3.7 27.8 - - - +
150B LYS* 3.7 17.5 - - + +
151B ARG* 1.3 78.0 - - - +
153B GLY* 1.3 56.5 + - - +
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Residues in contact with GLY 153 (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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15B ASP* 3.7 9.3 - - - +
17B ALA* 3.5 17.0 - - - -
143B SER 4.5 0.7 - - - -
144B VAL* 3.4 4.2 - - - +
145B LEU* 2.8 37.3 + - - +
151B ARG* 3.8 2.4 - - - +
152B LEU* 1.3 81.5 - - - +
154B CYS* 1.3 63.4 - - - +
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Residues in contact with CYS 154 (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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9B ASN* 3.3 9.9 + - - +
10B CYS* 2.1 67.2 + - + -
11B ASP* 4.7 0.9 - - - +
15B ASP* 3.7 14.3 + - - +
17B ALA 4.5 2.2 + - - -
142B GLU* 4.2 8.7 - - - -
143B SER 3.3 6.3 - - - -
144B VAL* 3.7 14.6 - - + -
151B ARG* 3.7 28.5 - - - +
153B GLY* 1.3 75.0 - - - +
155B ILE* 1.3 66.5 + - - +
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Residues in contact with ILE 155 (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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7B TRP* 5.4 1.8 - - + -
8B ASP 3.4 9.6 - - - +
9B ASN* 3.5 14.4 - - - +
10B CYS* 3.4 1.5 - - - -
18B VAL* 5.4 1.3 - - - -
19B ILE* 3.5 39.5 - - + +
22B LEU* 5.9 1.8 - - + -
141B ILE* 3.9 0.6 - - + +
142B GLU* 3.3 4.0 - - - +
143B SER* 2.8 49.7 + - - +
154B CYS* 1.3 81.2 - - - +
156B LYS* 1.3 66.6 - - - +
157B ILE* 4.2 24.0 - - + -
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Residues in contact with LYS 156 (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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7B TRP* 3.2 6.8 - - - +
8B ASP* 2.9 38.2 + - + +
10B CYS* 3.8 26.3 - - + +
141B ILE 3.2 5.8 - - - +
142B GLU* 3.3 33.6 + - + -
155B ILE* 1.3 77.4 - - - +
157B ILE* 1.3 64.5 + - - +
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Residues in contact with ILE 157 (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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5B PHE* 3.9 15.7 - - + -
6B SER 3.6 11.0 - - - +
7B TRP* 4.1 2.7 - - + -
22B LEU* 3.7 26.2 - - + -
24B LEU* 5.4 4.0 - - + -
140B ARG* 3.2 6.3 - - - +
141B ILE* 2.8 52.3 + - + +
155B ILE* 4.2 25.1 - - + -
156B LYS* 1.3 80.5 - - - +
158B ALA* 1.3 72.7 + - - +
159B ALA* 4.7 5.6 - - + +
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Residues in contact with ALA 158 (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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4B SER 4.0 14.6 - - - +
5B PHE* 3.2 9.1 - - - -
6B SER* 2.9 36.2 + - - +
65B TRP* 6.1 1.3 - - + -
139B TYR 3.4 9.6 - - - +
140B ARG* 4.5 11.0 - - + +
157B ILE* 1.3 74.5 - - - +
159B ALA* 1.3 63.9 + - - +
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Residues in contact with ALA 159 (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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4B SER 4.8 1.3 - - - -
5B PHE* 4.5 10.3 - - + +
24B LEU* 4.3 24.0 - - + -
29B ILE* 4.4 10.3 - - + -
138B ASN* 3.9 0.3 - - - +
139B TYR* 2.9 39.7 + - + +
157B ILE* 4.3 5.6 - - + -
158B ALA* 1.3 76.2 - - - +
160B SER* 1.3 64.1 + - - +
161B LEU* 5.7 2.2 - - + -
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Residues in contact with SER 160 (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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3B SER* 3.8 21.5 + - - -
4B SER* 4.3 2.6 + - - -
5B PHE* 5.3 0.4 - - - +
27B ASP* 4.3 9.9 + - - -
28B PRO* 3.4 19.6 - - - +
29B ILE* 2.8 35.4 + - - +
137B GLY 3.4 4.9 - - - -
138B ASN* 2.9 25.4 + - - +
159B ALA* 1.3 77.3 + - - +
161B LEU* 1.3 58.9 + - - +
162B LYS* 6.2 0.2 - - - -
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Residues in contact with LEU 161 (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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28B PRO* 4.4 0.6 - - - +
29B ILE* 3.3 39.0 - - + +
31B VAL* 4.1 11.4 - - + -
125B VAL* 6.0 1.3 - - + -
128B LEU* 4.0 25.6 - - + -
135B THR* 3.7 18.8 - - - +
136B THR* 3.3 4.1 - - - +
137B GLY 2.9 30.1 + - - +
139B TYR* 3.8 26.9 - - + -
159B ALA* 4.3 2.4 + - + -
160B SER* 1.3 77.3 - - - +
162B LYS* 1.3 67.5 + - - +
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Residues in contact with LYS 162 (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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28B PRO* 3.6 32.8 - - + -
29B ILE 2.8 9.8 + - - +
30B VAL* 3.3 17.4 - - + +
31B VAL* 3.0 24.9 + - - +
136B THR* 3.9 15.0 - - + +
160B SER* 6.2 0.2 - - - -
161B LEU* 1.3 83.6 - - - +
163B GLY* 1.3 58.6 + - - +
164B ILE 4.0 0.9 - - - -
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Residues in contact with GLY 163 (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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31B VAL* 3.5 12.1 - - - -
132B SER* 2.9 22.1 + - - -
135B THR* 3.7 17.6 + - - -
136B THR* 2.8 17.1 + - - -
161B LEU 4.1 0.2 - - - -
162B LYS* 1.3 74.8 - - - +
164B ILE* 1.3 70.3 + - - +
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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