Contacts of the strand formed by residues 150 - 162 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C LYS* 5.9 5.1 - - - +
16C PRO* 6.3 2.0 - - + -
146C SER* 3.3 1.9 - - - -
147C SER* 2.9 33.7 + - - +
148C SER 3.3 2.5 + - - +
149C GLY* 1.3 76.8 - - - +
151C ARG* 1.3 74.5 + - - +
152C LEU* 3.4 12.1 + - + +
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Residues in contact with ARG 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C CYS* 4.7 0.4 - - - +
11C ASP* 2.3 46.7 + - - +
14C LYS* 5.7 0.8 - - - +
15C ASP* 2.7 32.9 + - - +
16C PRO* 4.0 11.6 - - - +
144C VAL* 4.0 22.0 - - + +
145C LEU 3.8 4.7 - - - +
146C SER* 4.1 4.9 - - - -
149C GLY 3.7 3.4 + - - -
150C LYS* 1.3 85.4 - - - +
152C LEU* 1.3 63.4 + - - +
153C GLY 3.8 10.3 - - - +
154C CYS* 3.7 23.0 - - - +
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Residues in contact with LEU 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ASP* 3.2 10.8 - - - +
16C PRO* 3.2 7.3 - - + +
17C ALA* 2.8 30.3 + - + -
45C VAL* 4.1 24.2 - - + -
46C PRO 5.3 2.0 - - - +
47C LEU* 3.8 19.3 - - + -
48C SER 5.6 0.2 - - - +
51C LEU* 3.5 31.2 - - + -
145C LEU* 2.7 25.2 + - + +
146C SER* 3.9 6.3 - - - -
147C SER* 3.7 18.6 - - - +
150C LYS* 3.9 19.7 - - + +
151C ARG* 1.3 80.5 - - - +
153C GLY* 1.3 55.2 + - - +
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Residues in contact with GLY 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ASP* 3.7 8.5 - - - -
17C ALA* 3.4 19.3 - - - -
143C SER 4.5 0.4 - - - -
144C VAL* 3.5 4.7 - - - +
145C LEU* 2.8 37.5 + - - +
151C ARG* 3.7 2.1 - - - +
152C LEU* 1.3 80.0 - - - +
154C CYS* 1.3 61.9 + - - +
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Residues in contact with CYS 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ASN* 3.3 6.4 - - - +
10C CYS* 2.0 66.8 + - + -
11C ASP 4.7 0.2 + - - -
15C ASP* 3.6 5.9 + - - +
17C ALA 4.5 2.2 + - - -
142C GLU* 4.0 9.9 - - - -
143C SER 3.3 7.2 - - - -
144C VAL* 3.6 22.7 - - + -
151C ARG* 3.7 25.8 - - - +
153C GLY* 1.3 75.0 - - - +
155C ILE* 1.3 69.7 + - - +
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Residues in contact with ILE 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C TRP* 5.4 2.0 - - + -
8C ASP 3.4 9.2 - - - +
9C ASN* 3.6 21.8 - - - +
10C CYS* 3.5 0.9 - - - -
17C ALA 6.0 0.2 - - - +
18C VAL* 5.8 0.4 - - - -
19C ILE* 3.8 28.9 - - + +
22C LEU* 5.5 3.6 - - + -
141C ILE* 3.9 0.7 - - + +
142C GLU* 3.3 4.9 - - - +
143C SER* 2.9 48.3 + - - +
154C CYS* 1.3 83.4 - - - +
156C LYS* 1.3 66.1 + - - +
157C ILE* 4.1 25.4 - - + -
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Residues in contact with LYS 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C TRP* 3.1 4.5 - - - -
8C ASP* 2.9 37.5 + - + +
10C CYS* 3.9 21.8 - - + -
140C ARG* 6.2 2.0 - - - -
141C ILE 3.2 5.4 - - - +
142C GLU* 2.8 38.5 + - + +
155C ILE* 1.3 78.2 - - - +
157C ILE* 1.3 64.0 + - - +
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Residues in contact with ILE 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C PHE* 3.4 29.6 - - + -
6C SER 3.3 4.9 - - - +
7C TRP* 4.1 11.9 - - + +
22C LEU* 3.9 17.3 - - + -
24C LEU* 5.4 2.0 - - + -
140C ARG* 3.2 4.2 - - - +
141C ILE* 2.8 52.6 + - + +
155C ILE* 4.1 23.8 - - + -
156C LYS* 1.3 80.0 - - - +
158C ALA* 1.3 67.7 + - - +
159C ALA* 4.8 4.3 - - + +
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Residues in contact with ALA 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C SER 4.1 6.3 - - - +
5C PHE* 3.4 6.6 - - - -
6C SER* 2.8 46.7 + - - +
65C TRP* 5.8 2.7 - - + -
139C TYR 3.4 10.8 - - - +
140C ARG* 4.5 7.2 - - + -
157C ILE* 1.3 75.3 - - - +
159C ALA* 1.3 64.2 + - - +
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Residues in contact with ALA 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C SER 4.3 5.4 - - - -
5C PHE* 4.2 17.7 - - + +
24C LEU* 4.7 4.0 - - + -
29C ILE* 4.4 20.2 - - + -
138C ASN* 3.7 0.9 - - - +
139C TYR* 2.8 42.5 + - + +
157C ILE* 4.3 4.4 + - + -
158C ALA* 1.3 76.9 - - - +
160C SER* 1.3 61.3 + - - +
161C LEU* 5.3 2.9 - - + -
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Residues in contact with SER 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C SER 3.6 18.8 + - - -
27C ASP* 4.3 11.3 + - - -
28C PRO* 3.2 17.4 - - - +
29C ILE* 2.8 32.1 + - - +
137C GLY 3.4 6.3 - - - -
138C ASN* 2.8 25.8 + - - +
159C ALA* 1.3 75.4 - - - +
161C LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PRO* 4.3 2.0 - - - +
29C ILE* 3.4 28.5 - - + +
31C VAL* 3.2 36.6 - - + -
134C LEU* 4.6 22.7 - - + -
135C THR 4.3 7.4 - - - +
136C THR* 3.3 5.3 - - - +
137C GLY 2.8 30.2 + - - +
139C TYR* 3.9 25.8 - - + -
159C ALA* 4.3 3.3 + - + -
160C SER* 1.3 83.7 - - - +
162C LYS* 1.3 61.2 + - - +
163C GLY* 6.2 0.2 - - - -
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Residues in contact with LYS 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PRO* 3.7 24.5 - - + -
29C ILE 2.8 10.2 + - - +
30C VAL* 3.3 23.6 - - + +
31C VAL 3.1 23.9 + - - -
136C THR* 3.6 13.7 - - + +
161C LEU* 1.3 77.7 - - - +
163C GLY* 1.3 82.8 + - - +
164C ILE* 3.7 16.2 + - - +
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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