Contacts of the strand formed by residues 17 - 24 (chain A) in PDB entry 5FSJ
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 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.6 25.5 - - + +
10A GLY 3.2 13.0 - - - +
11A ARG* 4.0 16.0 + - - +
15A GLY 3.9 2.4 + - - -
16A ASP* 1.3 75.3 - - - +
18A LYS* 1.3 67.6 + - - +
19A ASN* 5.3 1.2 + - - -
63A PHE* 3.8 20.5 - - + -
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Residues in contact with LYS 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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9A VAL* 3.5 3.2 - - - -
10A GLY 2.9 31.9 + - - +
12A GLY 4.2 2.7 - - - +
16A ASP* 2.6 48.2 + - - -
17A GLN* 1.3 75.9 - - - +
19A ASN* 1.3 65.7 + - - +
20A ILE* 4.0 1.7 + - + +
71A VAL* 3.8 17.4 - - + +
72A ASP* 2.7 28.9 + - - +
75A TYR* 3.6 46.1 - - + +
76A TYR* 3.3 17.8 + - - -
182A LYS* 5.9 0.4 - - - +
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Residues in contact with ASN 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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7A VAL* 3.9 19.5 - - + +
8A GLY 3.3 10.2 - - - +
9A VAL* 3.7 19.2 - - - +
17A GLN* 5.3 1.4 + - - -
18A LYS* 1.3 74.1 - - - +
20A ILE* 1.3 60.8 + - - +
75A TYR* 3.3 27.9 - - + -
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Residues in contact with ILE 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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7A VAL* 3.5 4.9 - - - -
8A GLY 2.8 42.6 + - - +
9A VAL* 4.4 2.2 - - - +
18A LYS* 4.7 3.8 - - + +
19A ASN* 1.3 79.7 - - - +
21A ASN* 1.3 64.0 + - - +
22A THR* 3.5 2.4 + - + +
30A LEU* 3.5 28.0 - - + -
62A PHE* 3.6 26.7 - - + -
71A VAL* 4.0 39.7 - - + +
74A HIS* 4.1 16.4 - - + -
75A TYR* 4.1 16.2 - - + +
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Residues in contact with ASN 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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6A THR 3.6 4.9 + - - +
7A VAL* 4.1 19.8 - - - +
20A ILE* 1.3 73.3 - - - +
22A THR* 1.3 61.6 + - - +
31A GLN 3.5 5.9 - - - +
32A ASP* 3.2 29.2 - - + +
33A ASN 5.0 0.9 - - - +
34A THR* 3.7 20.5 + - + +
35A ARG* 3.4 23.6 + - - -
74A HIS* 2.8 31.6 + - - -
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Residues in contact with THR 22 (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 SER* 3.6 5.4 - - - -
6A THR* 2.7 48.9 + - - +
8A GLY 3.7 1.3 + - - +
20A ILE* 3.5 11.6 + - + +
21A ASN* 1.3 79.7 - - - +
23A THR* 1.3 59.4 + - - +
28A TYR* 4.7 0.7 - - - -
29A TYR 3.2 20.2 - - - +
30A LEU* 3.9 20.6 - - + -
31A GLN 3.1 10.9 - - - +
32A ASP* 5.3 0.2 - - - -
33A ASN* 4.3 0.7 + - - -
60A ASN* 2.8 27.8 + - - +
62A PHE* 4.1 10.8 - - + -
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Residues in contact with THR 23 (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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1A ILE* 3.5 26.2 - - + -
3A GLY* 3.7 24.9 - - - +
4A THR 3.4 4.9 - - - +
6A THR* 3.8 2.5 - - - -
22A THR* 1.3 70.5 - - - +
24A TYR* 1.3 62.3 + - - +
27A TYR 3.5 1.9 - - - +
28A TYR* 3.4 1.7 - - - -
29A TYR* 2.8 37.6 + - - -
31A GLN* 2.8 43.9 + - - +
33A ASN* 2.8 19.5 + - - +
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Residues in contact with TYR 24 (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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3A GLY* 3.3 2.4 - - - -
4A THR* 2.9 41.7 + - + +
6A THR* 3.7 23.0 + - + -
23A THR* 1.3 72.7 - - - +
25A SER* 1.3 64.6 + - - +
26A THR* 3.5 37.0 + - - -
27A TYR 3.4 10.8 - - - -
28A TYR* 3.5 39.5 - + + -
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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