Contacts of the strand formed by residues 16 - 24 (chain A) in PDB entry 4CFE
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 TYR 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A LYS* 3.3 4.0 - - - +
13A ILE* 2.8 44.6 + - + +
14A GLY 3.0 21.5 + - - -
15A HIS* 1.3 80.1 - - + +
17A VAL* 1.3 63.2 + - - +
18A LEU* 3.7 2.8 + - + -
33A GLY* 4.0 3.6 - - - -
34A GLU 3.7 5.6 - - - +
35A HIS* 3.6 35.9 - + + -
40A HIS* 2.8 45.6 + - - -
42A VAL* 3.5 37.8 - - + +
44A VAL* 5.6 1.8 - - + -
80A TYR* 5.7 0.9 - - - -
81A GLN* 5.3 8.3 - - - -
92A VAL* 4.7 13.7 - - + -
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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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10A ARG* 3.6 44.0 - - + +
11A VAL 3.4 9.9 - - - +
12A LYS* 3.9 15.5 - - + -
16A TYR* 1.3 73.0 - - - +
18A LEU* 1.3 71.4 + - - +
19A GLY 3.8 0.5 + - - -
32A ILE* 5.8 0.2 - - - +
33A GLY* 3.3 1.9 - - - -
34A GLU* 2.8 48.0 + - + +
36A GLN* 4.4 19.3 - - + -
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Residues in contact with LEU 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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10A ARG* 5.9 0.2 - - - +
11A VAL* 2.9 40.3 + - + +
13A ILE* 3.6 34.5 - - + -
16A TYR* 4.9 1.8 - - + +
17A VAL* 1.3 82.3 - - - +
19A GLY* 1.3 59.1 + - - +
31A LYS* 4.4 23.3 - - + -
32A ILE 3.4 8.3 - - - +
33A GLY* 4.3 4.7 - - - -
44A VAL* 3.8 29.6 - - + -
46A ILE* 4.7 3.1 - - + -
90A PHE* 4.2 18.6 - - + -
115B ILE* 4.9 1.1 - - + -
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Residues in contact with GLY 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 3.8 1.0 + - - -
18A LEU* 1.3 75.6 - - - +
20A ASP* 1.3 69.7 + - - +
21A THR 3.7 0.5 + - - -
31A LYS* 3.9 17.8 + - - +
32A ILE* 2.8 20.7 + - - -
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Residues in contact with ASP 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 GLY* 1.3 73.4 - - - -
21A THR* 1.3 65.7 + - - +
22A LEU* 3.4 2.6 + - + +
31A LYS* 3.9 0.2 - - - -
32A ILE* 3.0 34.8 + - + +
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Residues in contact with THR 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 GLY 3.7 0.6 + - - -
20A ASP* 1.3 74.5 - - - +
22A LEU* 1.3 60.6 + - - +
23A GLY* 3.3 27.7 + - - +
24A VAL* 4.5 1.3 - - + +
29A LYS* 3.9 18.6 - - + +
30A VAL 3.3 8.1 - - - +
31A LYS* 3.4 26.5 + - - -
108B SEP 3.6 18.9 + - - +
109B HIS* 6.2 2.5 - - - -
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Residues in contact with LEU 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 ASP* 3.4 2.1 + - + +
21A THR* 1.3 74.7 - - - +
23A GLY* 1.3 55.9 + - - +
30A VAL* 2.7 19.7 + - + +
32A ILE* 3.8 31.0 - - + +
43A ALA* 3.9 20.0 - - + -
95A TYR* 3.8 42.0 - - + +
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Residues in contact with GLY 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 THR* 3.2 13.3 - - - -
22A LEU* 1.3 80.8 - - - +
24A VAL* 1.3 61.6 + - - -
25A GLY 3.9 0.2 + - - -
30A VAL* 2.9 33.0 + - - +
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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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21A THR* 4.5 1.5 - - + +
23A GLY* 1.3 73.2 - - - -
25A GLY* 1.3 70.6 + - - +
28A GLY 3.4 19.7 - - - +
29A LYS* 4.5 14.1 - - + +
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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