Contacts of the strand formed by residues 94 - 100 (chain A) in PDB entry 1P0P
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 TYR 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLY* 3.8 15.5 - - - -
31A ILE 3.2 7.0 - - - +
32A PRO* 3.5 35.2 - - + -
33A TYR* 3.5 6.4 - - - -
36A PRO* 4.8 3.6 - - + +
56A TRP* 4.0 19.6 - + - -
62A ALA* 3.3 32.8 - - + -
63A ASN* 4.6 2.6 + - - -
91A ASP* 2.5 51.9 + - - -
92A CYS* 2.9 18.7 + - - +
93A LEU* 1.3 78.2 - - - +
95A LEU* 1.3 62.1 + - - +
96A ASN* 5.6 0.7 - - - +
123A SER* 5.1 0.3 + - - -
144A MET* 3.6 0.2 - - - -
145A ASN* 3.0 30.6 + - - +
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Residues in contact with LEU 95 (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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28A PHE 4.0 0.5 - - - +
30A GLY 3.3 4.5 + - - -
31A ILE* 2.8 53.8 + - + +
33A TYR* 3.9 20.9 - - + -
94A TYR* 1.3 75.4 - - - +
96A ASN* 1.3 70.3 + - - +
97A VAL* 3.9 20.0 - - + -
142A VAL* 4.7 8.7 - - + -
143A SER 3.2 14.4 - - - +
144A MET* 3.7 9.2 - - + +
174A ALA* 4.3 12.8 - - + +
177A TRP* 3.7 38.8 - - + -
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Residues in contact with ASN 96 (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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28A PHE 3.4 4.0 - - - -
29A LEU* 3.5 10.0 - - + -
30A GLY* 3.0 26.9 + - - -
61A TYR* 3.8 23.0 - - - -
62A ALA 5.1 0.7 + - - -
94A TYR 5.6 0.3 - - - -
95A LEU* 1.3 76.7 - - - +
97A VAL* 1.3 68.5 + - - +
98A TRP* 3.8 15.9 - - + -
123A SER* 3.1 27.7 + - - -
141A VAL 4.3 0.4 - - - -
142A VAL* 3.2 26.3 - - - +
143A SER* 2.7 34.3 + - - +
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Residues in contact with VAL 97 (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 THR 3.7 1.0 - - - +
27A ALA* 3.4 4.0 - - - +
28A PHE* 2.8 45.7 + - + +
29A LEU* 5.0 0.2 - - - +
31A ILE* 4.0 13.2 - - + -
95A LEU* 3.9 18.8 - - + -
96A ASN* 1.3 81.8 - - - +
98A TRP* 1.3 65.7 + - - +
99A ILE* 3.5 24.5 - - + -
140A ILE* 4.0 15.7 - - + -
141A VAL 3.3 3.1 - - - +
142A VAL* 4.2 10.8 - - + -
177A TRP* 4.2 11.4 - - + -
182A ILE* 4.5 4.7 - - + -
185A PHE* 4.2 11.7 - - + -
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Residues in contact with TRP 98 (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 LEU* 4.4 0.2 - - + -
25A VAL* 4.1 4.9 - - + -
26A THR 3.6 2.5 - - - -
27A ALA* 3.7 19.6 - - + +
29A LEU* 3.8 12.6 - - + -
61A TYR* 3.7 24.2 - + - -
96A ASN* 3.8 17.9 - - + -
97A VAL* 1.3 76.2 - - - +
99A ILE* 1.3 61.2 + - - +
123A SER 4.8 2.0 - - - -
128A TYR 4.0 9.6 - - - -
129A ASP* 3.4 8.9 + - - -
130A GLY* 3.5 34.3 - - - +
131A LYS* 3.5 22.4 - - + -
134A ALA* 3.9 17.8 - - + +
140A ILE* 3.3 6.9 - - - +
141A VAL* 2.8 58.2 + - + +
143A SER* 3.7 22.0 - - - -
602A GOL 2.8 20.3 + - - -
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Residues in contact with ILE 99 (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 ILE* 5.6 6.1 - - + -
6A ILE* 5.7 2.7 - - + -
25A VAL* 3.5 3.1 - - - +
26A THR* 2.9 48.0 + - + +
28A PHE* 4.5 11.2 - - + -
97A VAL* 3.5 23.6 - - + -
98A TRP* 1.3 78.4 - - - +
100A PRO* 1.3 81.6 - - + +
103A LYS* 4.4 18.4 - - + -
104A PRO* 4.5 0.9 - - + -
134A ALA* 4.3 2.9 - - - -
140A ILE* 4.2 9.6 - - + -
185A PHE* 3.8 37.7 - - + +
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Residues in contact with PRO 100 (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 THR 4.8 2.2 - - - +
25A VAL* 5.0 1.3 - - + -
26A THR* 4.6 0.3 + - - -
99A ILE* 1.3 100.4 - - + +
101A ALA* 1.3 60.1 + - - +
102A PRO 3.3 9.6 - - - +
103A LYS* 3.6 1.9 + - - -
104A PRO* 3.5 23.7 - - + +
134A ALA* 3.2 29.6 - - + +
135A ARG* 5.8 0.2 - - - -
138A ARG* 3.5 50.0 - - + +
139A VAL 3.6 10.1 - - - +
140A ILE* 3.9 5.4 - - + -
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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