Contacts of the strand formed by residues 15 - 25 (chain A) in PDB entry 6V65
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 ALA 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A SER* 3.4 7.5 + - - -
14A TYR* 1.3 79.8 - - - +
16A ARG* 1.3 63.6 + - - +
17A VAL* 5.4 0.9 - - + -
42A VAL 4.6 1.1 - - - -
43A THR* 3.6 3.6 - - - -
44A VAL* 3.3 27.6 + - + +
111A ALA* 3.9 23.1 - - + +
112A PHE* 4.1 20.9 - - + +
115A GLY* 4.0 8.5 - - - -
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Residues in contact with ARG 16 (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 SER* 4.1 15.1 + - - +
15A ALA* 1.3 78.4 - - - +
17A VAL* 1.3 69.5 + - - +
41A SER* 5.5 10.9 + - - -
42A VAL 3.6 3.6 - - - +
43A THR* 3.8 27.0 - - + +
63A GLU* 6.0 0.6 + - - -
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Residues in contact with VAL 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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15A ALA* 5.4 0.4 - - + -
16A ARG* 1.3 81.9 - - - +
18A ARG* 1.3 67.6 + - - +
19A ALA* 4.5 3.8 - - + -
41A SER* 3.3 6.4 - - - -
42A VAL* 2.9 36.9 + - + +
103A PHE* 3.8 20.6 - - + -
108A ASP* 3.5 42.6 - - + +
111A ALA* 5.2 4.5 - - + -
112A PHE* 3.7 33.8 - - + +
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Residues in contact with ARG 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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17A VAL* 1.3 79.5 - - - +
19A ALA* 1.3 62.1 + - - +
39A LEU* 4.2 9.6 - - + -
40A SER 3.3 9.6 - - - +
41A SER* 4.2 6.7 - - - +
65A LEU* 3.3 42.4 - - + +
103A PHE* 5.1 0.7 - - - -
104A GLN* 3.9 35.0 + - - +
108A ASP* 4.7 9.1 + - - +
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Residues in contact with ALA 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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17A VAL* 4.1 7.3 + - + -
18A ARG* 1.3 75.5 - - - +
20A VAL* 1.3 61.6 + - - +
21A VAL 4.0 0.2 + - - -
39A LEU* 3.4 10.5 - - - +
40A SER* 2.7 35.2 + - - +
42A VAL* 4.5 6.3 - - + +
101A LEU* 4.5 14.8 - - + -
102A THR 3.1 21.1 - - - +
103A PHE* 4.1 19.5 - - + +
104A GLN* 5.4 1.8 - - - +
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Residues in contact with VAL 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 ALA* 1.3 74.0 - - - +
21A VAL* 1.3 63.9 + - + +
22A MET* 3.6 23.8 + - + +
33A PRO* 3.9 20.4 - - + -
37A SER 5.5 0.2 - - - +
38A GLY 3.4 24.7 - - - +
39A LEU* 3.6 21.1 - - + -
101A LEU* 3.6 3.9 - - - -
102A THR* 3.1 35.2 + - - +
1250B ARG 4.0 21.1 - - - +
1251B HIS* 4.1 11.9 - - + +
1252B LEU* 4.7 0.2 - - + -
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Residues in contact with VAL 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 ALA 4.0 2.6 + - - -
20A VAL* 1.3 76.4 - - + +
22A MET* 1.3 67.8 + - - +
33A PRO* 3.2 22.2 - - - +
34A LEU* 3.3 25.9 + - + +
38A GLY 5.1 2.2 + - - +
40A SER* 4.5 9.0 + - - +
42A VAL* 5.6 2.0 - - + -
62A GLY* 6.6 0.2 - - - -
71A VAL* 3.7 27.8 - - + -
72A LEU* 3.7 38.1 - - + -
99A PHE* 5.6 1.3 - - + -
100A GLY 3.6 9.2 - - - +
101A LEU* 3.7 9.1 - - + +
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Residues in contact with MET 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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20A VAL* 3.6 31.4 - - + +
21A VAL* 1.3 78.6 - - - +
23A THR* 1.3 61.5 + - - +
31A TRP* 3.8 20.9 - - + +
32A LEU* 3.3 11.2 - - - +
33A PRO* 3.7 28.3 - - + -
34A LEU 5.1 0.2 - - - -
89A PHE* 4.6 4.5 - - + -
99A PHE* 3.5 4.3 - - - +
100A GLY* 2.7 43.8 + - - +
101A LEU 4.0 1.6 - - - +
102A THR* 3.1 49.6 - - + +
1215B MET* 5.3 4.9 - - - +
1252B LEU* 4.0 13.9 - - + -
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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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22A MET* 1.3 76.0 - - - +
24A ARG* 1.3 68.5 + - - +
25A ASP* 3.5 3.5 + - + +
31A TRP* 3.4 6.3 - - - -
32A LEU* 2.7 39.2 + - + +
33A PRO 4.2 2.7 - - - +
34A LEU* 4.0 33.9 - - + -
98A LYS 3.8 11.0 + - - -
99A PHE* 4.8 8.1 - - - -
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Residues in contact with ARG 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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23A THR* 1.3 78.5 + - - +
25A ASP* 1.3 71.8 + - - +
26A ASP* 3.8 23.2 + - - +
29A GLY* 4.8 16.8 + - - -
30A GLY* 3.5 11.0 - - - +
31A TRP* 3.1 36.0 - - + +
98A LYS* 3.9 36.9 + - + +
1217B ASP* 2.7 44.1 + - - -
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Residues in contact with ASP 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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23A THR* 3.5 4.5 + - + +
24A ARG* 1.3 75.5 - - - +
26A ASP* 1.3 55.4 + - - +
27A SER* 2.5 40.7 + - - -
28A SER* 3.3 27.8 + - - +
29A GLY* 2.7 33.1 + - - -
30A GLY 2.9 11.9 + - - +
32A LEU* 4.7 12.2 - - + +
1517B LYS* 5.5 0.2 + - - -
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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