Contacts of the strand formed by residues 14 - 23 (chain A) in PDB entry 3AEV
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 PHE 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A GLY 3.8 11.9 - - - -
13A GLU* 1.3 83.0 - - - +
15A VAL* 1.3 64.2 + - - +
65A VAL* 4.4 2.7 - - + -
66A ALA 3.4 4.9 - - - +
67A LYS* 3.6 44.0 - - + -
85A VAL* 4.2 17.7 - - + -
89A GLN* 3.4 52.9 - - + -
93A LYS* 3.2 43.0 + - + +
96A GLU* 5.1 0.5 - - - +
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Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PRO* 4.1 9.6 - - + -
13A GLU* 4.1 16.4 - - + +
14A PHE* 1.3 80.3 - - - +
16A VAL* 1.3 66.2 + - - +
17A ALA* 3.9 0.4 + - + -
31A LEU* 3.8 26.7 - - + -
33A GLU* 3.5 11.2 - - - +
34A TYR* 4.5 5.6 - - + -
64A VAL 3.6 0.2 - - - +
65A VAL* 3.3 4.9 - - - -
66A ALA* 2.9 41.6 + - + +
68A VAL* 3.8 20.2 - - + -
80A LEU* 3.9 19.3 - - + -
93A LYS* 4.0 2.7 - - - +
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Residues in contact with VAL 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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15A VAL* 1.3 78.6 - - - +
17A ALA* 1.3 61.9 + - - +
31A LEU* 3.8 3.1 - - - +
32A ASP* 3.0 41.1 + - + +
33A GLU* 3.2 10.3 + - - +
63A LYS* 4.1 7.9 - - + -
64A VAL 3.3 4.3 - - - +
65A VAL* 4.7 2.9 - - + -
93A LYS* 4.0 17.0 - - + -
94A LEU* 5.0 1.1 - - + -
97A PHE* 3.6 44.4 - - + -
31B PHE* 3.8 33.0 - - + -
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Residues in contact with ALA 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 VAL* 4.8 2.9 - - + +
16A VAL* 1.3 77.8 - - - +
18A THR* 1.3 65.7 + - - +
19A VAL 4.2 0.2 - - - -
29A LEU* 3.9 24.0 - - + -
30A GLU 3.3 11.7 - - - +
31A LEU* 3.9 17.3 - - + -
32A ASP* 3.8 2.5 - - - -
62A GLN 3.8 0.5 - - - +
63A LYS* 3.4 4.0 - - - +
64A VAL* 2.8 38.9 + - + +
66A ALA* 5.3 0.2 - - + -
80A LEU* 4.1 7.0 - - + -
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Residues in contact with THR 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 ALA* 1.3 74.1 - - - +
19A VAL* 1.3 69.1 + - - +
20A LYS* 3.2 24.2 + - - +
29A LEU* 3.0 5.5 - - - -
30A GLU* 2.7 42.3 + - - -
32A ASP* 2.6 23.5 + - - -
61A GLY* 3.5 28.3 - - - +
62A GLN 3.4 2.9 - - - +
63A LYS* 3.0 23.8 + - - +
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Residues in contact with VAL 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 THR* 1.3 68.8 - - - +
20A LYS* 1.3 64.5 + - - +
21A ARG 4.4 3.6 - - - +
22A ILE* 3.8 31.2 - - + -
27A ALA* 4.6 4.5 - - + -
28A PHE 4.4 2.9 - - - +
29A LEU* 3.9 22.4 - - + -
58A LEU* 4.2 24.0 - - + -
59A LYS 3.4 23.6 - - - +
60A GLU* 3.7 2.7 - - - -
61A GLY* 2.8 29.3 + - - -
62A GLN* 2.9 26.6 + - + +
64A VAL* 5.1 3.6 - - + -
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Residues in contact with LYS 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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18A THR* 3.2 27.8 + - + +
19A VAL* 1.3 81.1 - - - +
21A ARG* 1.3 77.6 + - - +
28A PHE 2.9 12.8 + - - +
29A LEU 4.9 0.2 - - - -
30A GLU* 3.7 37.8 + - + +
38A GLU* 4.8 10.1 - - - +
60A GLU* 4.2 13.5 - - - +
61A GLY* 5.7 1.9 - - - +
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Residues in contact with ARG 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 VAL 3.9 0.6 - - - -
20A LYS* 1.3 87.1 - - + +
22A ILE* 1.3 64.6 + - - +
23A HIS* 4.1 23.9 + - + +
27A ALA* 3.2 6.9 - - - +
28A PHE* 2.8 67.0 + - + +
38A GLU* 2.8 42.6 + - - -
60A GLU* 4.7 3.6 - - - -
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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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19A VAL* 3.8 15.7 - - + -
21A ARG* 1.3 80.0 - - - +
23A HIS* 1.3 81.3 + - - +
26A GLY 3.8 3.8 - - - +
27A ALA* 4.2 6.3 - - + -
53A ASN* 6.0 0.2 - - - +
54A ILE* 4.1 21.3 - - + -
55A ARG* 3.9 36.3 + - + +
58A LEU* 3.5 36.1 - - + +
60A GLU* 3.8 34.4 + - - +
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Residues in contact with HIS 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 ARG* 4.1 28.3 + - + +
22A ILE* 1.3 93.1 + - - +
24A ASN* 1.3 70.3 + - - +
25A TYR 3.3 3.6 - - - +
26A GLY* 2.8 22.2 + - - +
28A PHE* 3.8 36.9 - + - -
40A PHE* 5.9 0.4 - + - -
54A ILE* 4.1 4.5 - - - +
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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