Contacts of the strand formed by residues 19 - 25 (chain A) in PDB entry 6ULG
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 LEU 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A LEU* 3.7 27.3 - - + +
14A PRO* 5.5 1.9 - - - +
16A VAL* 3.4 39.9 + - + +
17A GLU 3.2 4.2 + - - -
18A GLY* 1.3 77.9 - - - +
20A HIS* 1.3 65.6 + - - +
21A ALA 4.5 2.9 - - - +
22A ILE* 3.7 31.9 - - + -
37A ASN* 4.5 8.0 + - - -
39A ASN* 5.5 0.2 + - - -
92A PHE* 4.2 17.3 - - + -
93A ILE 3.4 23.3 - - - +
94A ALA* 3.8 14.6 - - + -
103A ILE* 4.3 7.9 - - + -
106A LEU* 4.0 6.5 - - + -
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Residues in contact with HIS 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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13A LEU* 3.5 16.9 - - - +
18A GLY* 3.4 24.0 + - - -
19A LEU* 1.3 79.3 + - - +
21A ALA* 1.3 59.1 + - - +
22A ILE 4.3 0.4 - - - -
36A ALA* 3.6 6.6 - - - +
37A ASN* 3.1 18.0 - - - +
39A ASN* 3.5 35.2 + - + +
40A ALA* 3.7 34.3 - - + +
41A PRO* 4.8 6.5 - - + -
78A TYR* 5.8 2.2 - - + -
93A ILE* 2.8 18.1 + - + +
94A ALA 4.4 2.7 - - - -
95A SER* 4.1 22.1 - - - -
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Residues in contact with ALA 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 LEU* 4.5 0.8 - - - +
20A HIS* 1.3 74.6 - - - +
22A ILE* 1.3 61.8 - - - +
23A VAL* 3.9 0.7 + - - +
35A VAL 3.5 5.8 - - - +
36A ALA* 3.8 18.8 - - + -
40A ALA* 4.4 4.0 - - + -
45A LEU* 3.8 29.2 - - + -
91A SER 3.6 1.7 - - - +
92A PHE 3.5 1.7 - - - -
93A ILE* 2.7 51.1 + - + +
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Residues in contact with ILE 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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9A LEU* 4.4 26.2 - - + +
12A LYS* 5.2 2.0 - - + +
13A LEU* 3.7 28.9 - - + +
19A LEU* 3.7 21.3 - - + -
21A ALA* 1.3 73.0 - - - +
23A VAL* 1.3 65.0 + - - +
24A VAL* 5.4 1.1 - - + +
33A ILE* 4.1 0.7 - - - +
35A VAL* 3.2 35.8 + - + +
90A VAL* 5.2 2.5 - - + -
91A SER 3.7 3.4 - - - +
92A PHE* 3.6 38.4 - - + +
106A LEU* 4.1 9.2 - - + -
110A LEU* 4.9 7.4 - - + -
114A PHE* 5.2 12.3 - - + -
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Residues in contact with VAL 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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21A ALA 4.6 3.1 - - - +
22A ILE* 1.3 78.4 - - - +
24A VAL* 1.3 70.2 + - - +
31A PRO* 4.4 6.5 - - + -
33A ILE 3.3 16.8 - - - +
34A LYS* 3.8 25.1 - - + -
45A LEU* 3.9 15.5 - - + -
50A LEU* 3.7 33.4 - - + -
89A VAL 3.5 1.0 - - - +
90A VAL* 3.6 1.0 - - - +
91A SER* 2.6 58.6 + - - +
93A ILE* 5.0 3.1 - - + -
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Residues in contact with VAL 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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9A LEU* 6.4 0.9 - - + -
22A ILE* 5.4 2.2 - - + +
23A VAL* 1.3 87.7 - - - +
25A SER* 1.3 66.6 + - - +
31A PRO* 3.5 0.5 - - - +
32A VAL* 3.2 27.0 + - + -
33A ILE* 3.1 34.2 + - + +
88A LEU* 5.0 4.5 - - + -
89A VAL 3.3 4.9 - - - +
90A VAL* 3.9 18.6 - - + -
114A PHE* 3.6 36.6 - - + -
117A LEU* 4.0 18.6 - - + -
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Residues in contact with SER 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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24A VAL* 1.3 78.3 - - - +
26A ASP* 1.3 88.2 + - - +
29A GLY* 3.2 9.4 - - - -
30A VAL 3.0 30.4 + - - -
31A PRO* 4.2 1.3 - - - -
32A VAL* 4.1 9.4 - - - -
50A LEU* 4.9 14.6 - - - -
88A LEU* 3.3 15.4 - - - +
89A VAL* 3.0 32.1 + - - -
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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