Contacts of the strand formed by residues 14 - 19 (chain A) in PDB entry 3EDH
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 VAL 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A TRP* 3.6 16.1 - - - +
11A PRO* 3.0 14.9 + - - +
12A ASP* 3.8 18.8 - - + +
13A GLY* 1.3 76.4 - - - +
15A ILE* 1.3 62.5 + - - +
16A PRO* 3.5 14.2 - - + +
44A THR* 3.6 19.5 - - - +
46A LEU* 4.1 33.2 - - + -
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Residues in contact with ILE 15 (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 TRP* 3.6 37.5 - - + -
13A GLY 3.9 7.2 - - - +
14A VAL* 1.3 77.6 - - - +
16A PRO* 1.3 73.6 - - - +
17A PHE 3.7 0.5 + - - -
43A VAL* 3.6 23.8 - - + -
44A THR 2.8 12.9 + - - +
45A PHE* 3.3 32.9 - - + -
46A LEU 3.1 19.7 + - - -
55A ILE* 4.0 22.0 - - + -
97A VAL* 4.0 11.9 - - + -
98A VAL* 4.2 9.0 - - + -
194A TYR* 5.0 1.8 - - + +
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Residues in contact with PRO 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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10A TRP* 3.8 9.4 - - + -
14A VAL* 3.5 16.8 - - + +
15A ILE* 1.3 88.2 - - - +
17A PHE* 1.3 59.9 + - - +
46A LEU* 3.1 14.4 - - + +
48A ARG* 4.0 5.4 - - + -
51A GLU* 3.7 37.9 - - + +
53A SER 3.7 19.3 - - - +
54A TYR* 3.3 14.9 - - + +
55A ILE* 2.9 24.6 + - - +
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Residues in contact with PHE 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 ILE 4.2 1.1 - - - +
16A PRO* 1.3 75.7 - - - +
18A VAL* 1.3 66.8 + - - +
19A ILE* 4.0 27.6 - - + -
31A ARG* 3.6 9.0 - - - -
34A MET* 3.7 29.8 - - + -
45A PHE* 3.9 1.8 - - + -
46A LEU 2.9 46.2 + - - -
47A GLU* 3.3 40.2 - - - +
48A ARG* 2.9 23.8 + - - +
54A TYR* 4.9 0.2 - - - -
55A ILE* 3.2 29.6 - - + +
57A PHE* 4.2 5.6 - + + -
216A DMS 3.8 21.3 - - + -
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 1.3 80.8 - - - +
19A ILE* 1.3 77.0 + - - +
20A GLY* 4.4 2.2 - - - +
48A ARG* 3.8 19.3 - - + +
54A TYR* 3.7 22.4 - - + -
55A ILE 2.9 9.0 + - - +
56A VAL* 3.2 18.5 - - + -
57A PHE* 2.9 28.1 + - - -
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Residues in contact with ILE 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 PHE* 4.0 14.4 - - + -
18A VAL* 1.3 81.4 - - - +
20A GLY* 1.3 75.1 + - - +
22A PHE* 4.1 1.3 - - + -
27A ARG* 3.7 37.0 - - + +
30A PHE* 3.9 27.8 - - + -
31A ARG* 4.0 40.6 - - + +
34A MET* 4.8 0.9 - - + -
57A PHE* 3.9 19.3 - - + -
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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