Contacts of the strand formed by residues 14 - 21 (chain A) in PDB entry 4OD9
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 GLN 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LYS 3.7 1.2 - - - +
9A ASN* 3.6 2.4 - - - +
10A TYR* 2.8 59.0 + - + +
13A ALA* 1.3 88.3 - - + +
15A TYR* 1.3 63.0 + - - +
16A TYR* 3.8 6.7 - - + -
31A VAL* 5.2 0.4 - - + -
103A 2RZ 4.0 19.2 + - - +
128B ALA 5.3 1.0 + - - -
129B ALA* 3.5 13.8 - - - +
130B LYS* 2.8 32.3 + - - +
131B PHE* 3.6 31.1 - - + -
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Residues in contact with TYR 15 (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 LEU* 4.6 9.6 - - + -
8A LYS 3.3 6.5 - - - +
9A ASN* 3.4 23.6 - - + -
12A ASP* 3.4 25.2 + - - -
13A ALA 4.2 0.2 - - - -
14A GLN* 1.3 74.5 - - - +
16A TYR* 1.3 61.6 + - - +
31A VAL* 3.5 27.4 - - + +
32A PHE 4.3 2.6 + - - +
103A 2RZ 5.4 0.4 - - - -
167B PHE* 6.5 0.4 - - + -
169B LEU* 3.7 36.0 - - + +
170B SER 2.6 29.8 + - - -
171B ARG* 3.2 18.4 + - - -
178B GLY 3.5 18.4 - - - -
179B GLY* 5.1 1.3 - - - -
232B THR* 5.5 4.9 + - - +
323B ASP* 3.5 37.2 + - + -
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Residues in contact with TYR 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 3.4 8.3 - - - +
8A LYS* 2.8 70.4 + - + +
9A ASN 5.4 0.5 - - - -
10A TYR* 4.1 10.8 + - + +
14A GLN* 3.8 25.6 - - + -
15A TYR* 1.3 75.4 - - - +
17A GLY* 1.3 57.4 + - - +
29A THR* 3.8 30.5 - - + -
30A VAL 3.2 22.7 - - - +
31A VAL* 4.1 1.3 - - + +
32A PHE* 5.2 0.2 - - - -
130B LYS* 3.6 45.3 - - + +
131B PHE* 3.9 15.0 - - + -
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Residues in contact with GLY 17 (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 GLU* 3.4 12.8 - - - -
6A VAL 3.7 13.9 - - - -
7A LEU* 3.7 4.4 - - - +
8A LYS* 6.3 0.2 - - - -
16A TYR* 1.3 74.1 - - - +
18A GLU* 1.3 61.4 + - - -
19A ILE 3.8 0.3 + - - -
28A PHE 3.7 0.3 - - - +
29A THR* 3.3 5.7 - - - -
30A VAL* 2.9 35.6 + - - +
32A PHE* 3.8 6.5 - - - -
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Residues in contact with GLU 18 (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 GLU* 2.7 28.9 + - - +
6A VAL 4.6 1.4 + - - -
17A GLY* 1.3 72.7 - - - -
19A ILE* 1.3 63.8 + - - +
27A CYS* 3.7 24.6 - - + +
28A PHE 3.3 12.5 - - - +
29A THR* 4.4 11.5 - - + +
95A PRO* 3.6 11.8 - - + +
96A CYS* 3.8 20.0 + - + +
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Residues in contact with ILE 19 (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 GLU* 1.3 78.0 - - - +
20A GLY* 1.3 60.0 + - - +
21A ILE* 4.1 22.0 - - + -
27A CYS* 3.3 6.1 - - - +
28A PHE* 2.8 44.4 + - + +
30A VAL* 3.8 29.2 - - + -
32A PHE* 3.6 29.8 - - + -
39A LEU* 3.9 20.4 - - + -
92A VAL* 4.3 6.3 - - + -
93A SER 3.4 10.1 - - - +
94A VAL* 4.0 16.6 - - + -
96A CYS* 3.6 9.3 - - - +
135B LEU* 4.2 6.5 - - + -
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Residues in contact with GLY 20 (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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19A ILE* 1.3 73.8 - - - +
21A ILE* 1.3 64.8 + - - +
22A GLY 4.3 0.4 - - - -
25A PRO* 4.0 8.5 - - - -
26A GLN 3.2 7.9 - - - -
91A THR 4.4 0.2 - - - -
92A VAL* 3.3 6.9 - - - +
93A SER* 2.8 37.2 + - - +
96A CYS* 3.6 18.9 - - - +
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Residues in contact with ILE 21 (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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19A ILE* 4.1 15.7 - - + -
20A GLY* 1.3 79.3 - - - +
22A GLY* 1.3 64.5 + - - +
26A GLN* 2.9 38.0 + - - +
28A PHE* 4.0 14.6 - - + -
39A LEU* 4.5 8.7 - - + -
41A VAL* 3.7 42.8 - - + -
59A TYR* 3.7 12.6 - - + -
90A ASP* 3.8 7.2 - - + -
91A THR 3.4 5.4 - - - +
92A VAL* 4.4 9.0 - - + -
115B PHE* 3.6 41.7 - - + -
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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