Contacts of the strand formed by residues 110 - 119 (chain A) in PDB entry 1A9P
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 THR 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A GLN* 3.2 8.5 + - - -
27A VAL* 3.5 11.1 - - + -
28A ALA 2.9 25.2 + - - -
108A VAL* 3.2 8.0 - - - +
109A GLU* 1.3 79.4 - - - +
111A LEU* 1.3 69.6 + - - +
112A VAL* 4.3 9.4 - - + -
170A MET* 3.7 31.6 - - + -
233A LEU* 4.8 0.9 - - - -
234A ARG* 3.1 18.0 + - - +
282A ILE* 3.0 32.4 - - + +
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Residues in contact with LEU 111 (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 ALA* 3.3 28.5 - - + +
30A ILE* 3.9 25.4 - - + -
100A VAL* 4.5 7.2 - - + -
103A PHE* 4.0 13.2 - - + -
110A THR* 1.3 75.6 - - - +
112A VAL* 1.3 63.4 + - - +
113A VAL* 3.8 22.9 - - + -
224A GLU 4.4 7.0 - - - +
225A VAL* 5.3 0.2 - - - -
228A ALA* 3.6 28.0 - - + -
233A LEU* 4.4 15.0 - - + +
234A ARG 3.0 10.4 + - - +
235A VAL* 3.5 11.7 - - + +
236A PHE 3.2 22.7 + - - +
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Residues in contact with VAL 112 (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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27A VAL* 4.0 24.2 - - + -
28A ALA 2.9 5.2 + - - +
29A VAL* 3.5 26.8 - - + +
30A ILE* 3.1 22.7 + - - +
110A THR* 4.5 8.7 - - + -
111A LEU* 1.3 77.7 - - - +
113A VAL* 1.3 60.4 + - - +
114A THR* 4.6 10.3 - - + -
170A MET* 6.0 0.9 - - - -
236A PHE* 3.1 29.2 - - + +
238A PHE* 4.9 6.1 - - + -
275A VAL* 5.1 8.5 - - + -
278A LEU* 6.3 1.8 - - + -
279A MET* 5.8 2.5 - - - -
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Residues in contact with VAL 113 (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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30A ILE* 3.9 21.1 - - + -
84A ARG* 4.4 2.5 - - - +
111A LEU* 3.8 26.2 - - + -
112A VAL* 1.3 76.3 - - - +
114A THR* 1.3 64.7 + - - +
132A ILE* 4.8 3.5 - - + +
166A TYR* 4.9 1.3 - - + -
221A THR* 3.7 28.3 - - + -
224A GLU* 4.2 9.4 - - + +
225A VAL* 4.1 16.6 - - + -
235A VAL* 4.4 3.8 - - + -
236A PHE 2.9 18.4 + - - +
237A GLY* 2.9 31.8 - - - -
238A PHE* 3.1 5.4 + - - -
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Residues in contact with THR 114 (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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29A VAL* 4.8 0.9 - - + -
30A ILE 2.8 23.8 + - - +
31A CYS* 3.4 3.3 - - - -
32A GLY 3.2 13.3 + - - -
35A LEU* 3.5 13.5 - - - +
38A LEU* 4.5 13.3 - - + +
84A ARG* 2.9 27.6 + - - +
112A VAL* 4.6 9.6 - - + -
113A VAL* 1.3 79.5 - - - +
115A ASN* 1.3 65.1 + - - +
221A THR* 4.0 0.2 + - - -
238A PHE* 3.3 45.1 - - + -
275A VAL* 5.5 0.2 - - + -
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Residues in contact with ASN 115 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A GLY* 4.1 0.2 - - - -
35A LEU* 3.6 15.8 - - - +
84A ARG* 3.8 4.5 - - - +
114A THR* 1.3 79.7 + - - +
116A ALA* 1.3 64.4 + - - +
132A ILE* 4.1 8.1 - - - +
192A TYR* 3.6 22.3 - - - -
220A SER* 4.1 0.4 - - - +
221A THR* 2.7 36.2 + - - +
238A PHE 3.4 2.2 + - - +
239A SER* 2.8 25.8 + - - -
240A LEU 3.0 20.4 + - - -
291A PO4 3.2 19.7 - - - +
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Residues in contact with ALA 116 (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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33A SER* 3.8 19.5 - - - +
35A LEU* 4.3 0.6 - - + +
115A ASN* 1.3 77.2 - - - +
117A ALA* 1.3 61.3 + - - +
218A GLY* 4.7 2.8 - - - -
240A LEU* 3.5 7.4 - - + -
242A THR* 3.6 13.0 - - + -
259A GLU* 3.2 27.1 - - - +
290A 9DI 3.2 23.4 + - + -
291A PO4 2.7 16.0 + - - +
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Residues in contact with ALA 117 (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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115A ASN 4.1 0.4 - - - -
116A ALA* 1.3 74.6 - - - +
118A GLY* 1.3 61.9 + - - +
119A GLY 3.8 0.3 + - - -
192A TYR* 3.9 16.4 - - + -
216A ALA* 3.8 22.0 - - + -
217A VAL 3.4 15.0 - - - +
239A SER* 3.9 13.9 - - - -
240A LEU 3.0 8.1 + - - +
241A ILE* 3.5 8.0 - - + -
242A THR* 3.2 23.4 + - - -
243A ASN* 3.8 0.3 + - - +
290A 9DI 3.7 7.6 - - - -
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Residues in contact with GLY 118 (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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117A ALA* 1.3 72.5 - - - +
119A GLY* 1.3 61.7 + - - -
120A LEU 3.6 0.2 + - - -
216A ALA* 3.2 7.6 - - - -
217A VAL* 3.0 34.2 + - - +
241A ILE* 4.8 0.2 - - - -
243A ASN* 3.6 13.0 - - - -
245A VAL* 3.9 7.6 - - - -
290A 9DI 3.3 25.4 + - - -
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Residues in contact with GLY 119 (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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117A ALA 3.8 1.2 + - - -
118A GLY* 1.3 73.0 - - - -
120A LEU* 1.3 60.7 + - - -
121A ASN 3.7 3.8 - - - -
124A PHE* 4.6 7.0 - - - -
215A ASP 4.0 4.9 - - - -
241A ILE* 4.0 18.7 - - - +
243A ASN 2.8 18.3 + - - -
244A LYS* 4.2 9.3 + - - -
245A VAL* 3.1 27.8 + - - +
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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