Contacts of the strand formed by residues 24 - 33 (chain A) in PDB entry 6XYY
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 ARG 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A VAL 3.6 0.2 - - - +
20A THR* 3.3 5.8 - - - +
21A VAL 2.9 34.0 + - - +
22A GLN 4.4 4.7 - - - +
23A GLY* 1.3 81.6 - - - +
25A GLU* 1.3 67.9 + - - +
26A VAL* 3.6 3.5 + - - +
101A PRO* 5.1 8.1 - - - +
102A ALA* 5.6 7.2 - - - +
168A ALA 5.0 0.7 - - - -
169A ALA* 3.0 37.4 + - + +
170A VAL 5.6 0.2 + - - -
172A ASN* 3.5 43.1 + - - +
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Residues in contact with GLU 25 (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 ARG* 6.0 1.2 - - - +
5A LEU* 4.9 1.2 - - - +
18A SER* 2.7 30.6 + - - +
19A VAL 3.2 9.2 - - - +
20A THR* 4.4 9.3 - - - +
24A ARG* 1.3 74.2 - - - +
26A VAL* 1.3 55.6 + - - +
27A HIS* 3.4 24.5 + - - +
101A PRO* 3.8 2.1 - - - +
102A ALA* 2.8 46.6 + - + +
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Residues in contact with VAL 26 (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 SER* 3.4 2.6 - - - -
19A VAL* 2.8 48.7 + - + +
21A VAL* 4.9 1.1 - - + -
24A ARG* 4.1 5.2 - - + +
25A GLU* 1.3 78.1 - - - +
27A HIS* 1.3 69.6 + - - +
28A VAL* 4.0 4.5 - - + -
99A TRP* 4.1 11.7 - - + -
100A ALA 3.3 30.3 - - - +
101A PRO* 4.0 4.7 - - + -
165A ASP* 4.4 4.9 - - - +
168A ALA* 4.1 11.2 - - + -
169A ALA* 3.8 36.8 - - + +
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Residues in contact with HIS 27 (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 ARG* 3.9 18.9 + - + +
5A LEU* 3.3 33.3 - - + +
17A ARG 3.4 4.3 - - - +
18A SER* 3.8 9.2 - - - -
25A GLU* 3.4 25.4 + - + -
26A VAL* 1.3 79.9 - - - +
28A VAL* 1.3 61.0 + - - +
29A TYR* 3.4 39.7 + - + +
98A VAL 3.6 0.3 - - - +
100A ALA* 2.7 38.3 + - + +
101A PRO 5.3 0.8 + - - -
102A ALA* 4.7 17.6 - - - -
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Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY* 3.5 1.2 - - - -
17A ARG* 2.7 62.6 + - - +
19A VAL* 3.8 24.9 - - + -
26A VAL* 4.3 2.7 - - + +
27A HIS* 1.3 73.8 - - - +
29A TYR* 1.3 62.7 + - - +
30A THR* 4.0 20.9 + - + -
59A ALA 3.7 4.7 - - - +
98A VAL 3.8 3.1 - - - +
99A TRP* 3.5 39.5 - - + +
165A ASP* 3.8 9.2 - - - +
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Residues in contact with TYR 29 (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 LEU* 3.1 32.0 + - - -
6A VAL 4.9 0.5 - - - -
7A VAL* 3.9 22.9 - - + +
14A VAL* 4.1 8.3 - - + -
15A ARG 4.0 3.6 - - - -
16A GLY* 3.4 21.3 - - - -
27A HIS* 3.4 48.1 + - + +
28A VAL* 1.3 70.7 - - - +
30A THR* 1.3 60.9 + - - +
32A ILE* 3.9 21.0 - - + +
59A ALA* 3.6 7.6 - - + -
96A ILE 4.2 0.7 - - - +
97A ASN* 3.2 3.3 - - - +
98A VAL* 2.8 44.9 + - - +
100A ALA* 4.5 5.2 - - + -
225A PHE* 3.6 29.8 - + + -
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Residues in contact with THR 30 (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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17A ARG* 4.0 10.4 + - - +
28A VAL* 4.0 18.0 + - + -
29A TYR* 1.3 75.3 - - - +
31A GLY* 1.3 59.3 + - - +
32A ILE 3.7 1.1 - - - -
58A ASP 4.4 0.7 - - - +
59A ALA* 2.8 40.0 + - - +
60A THR 3.8 4.9 - - - -
61A GLY 2.9 29.6 + - - +
62A LEU* 4.5 15.7 - - + -
97A ASN* 3.2 26.7 - - + +
99A TRP* 4.7 8.1 - - + -
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Residues in contact with GLY 31 (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 THR* 1.3 74.4 - - - +
32A ILE* 1.3 63.0 + - - +
33A PRO* 3.8 4.7 - - - +
57A LEU* 4.2 12.4 - - - +
58A ASP 4.7 1.8 - - - +
61A GLY 4.1 3.6 + - - -
63A SER* 4.0 25.5 - - - -
95A TYR* 3.5 15.8 - - - -
96A ILE 3.2 2.5 + - - -
97A ASN* 3.1 12.1 + - - -
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Residues in contact with ILE 32 (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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14A VAL* 4.0 31.2 - - + -
29A TYR* 3.9 27.6 - - + +
31A GLY* 1.3 79.6 - - - +
33A PRO* 1.3 79.5 - - + +
34A TYR* 3.5 0.7 + - + -
53A TRP* 4.1 13.5 - - + -
57A LEU* 5.2 1.8 - - + -
59A ALA* 4.2 7.0 - - + -
95A TYR* 3.1 3.0 - - - -
96A ILE* 2.6 45.3 + - + +
98A VAL* 4.9 6.3 - - + -
217A TRP* 4.0 27.6 - - + -
225A PHE* 4.4 13.2 - - + -
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Residues in contact with PRO 33 (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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11A SER* 5.0 0.7 + - - -
31A GLY 3.8 4.7 - - - +
32A ILE* 1.3 92.4 - - + +
34A TYR* 1.3 60.7 + - - +
35A ALA 4.4 10.8 - - - +
37A PRO* 6.4 0.4 - - + -
50A ALA* 4.0 9.6 - - + +
53A TRP* 3.5 29.9 - - + -
57A LEU* 3.5 26.0 - - + -
94A LEU 3.6 3.8 - - - +
95A TYR* 3.6 25.1 - - + -
217A TRP* 4.6 4.9 + - - -
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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