Contacts of the strand formed by residues 56 - 60 (chain A) in PDB entry 4UML
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A SER* 3.2 5.2 + - - -
19A TRP* 2.6 46.5 + - + +
52A VAL 3.7 9.6 - - - +
53A ASN 3.5 7.5 + - - +
54A GLY 3.5 0.4 - - - -
55A LYS* 1.3 79.0 - - - +
57A VAL* 1.3 62.8 + - - +
58A LEU 4.9 0.4 - - - +
189A VAL* 5.1 0.4 - - + -
193A LEU* 4.0 10.8 - - + -
203A VAL* 3.5 4.9 - - + +
205A PHE* 4.0 25.6 - - + -
219A LEU* 4.1 17.3 - - + -
223A PHE* 3.5 37.5 - - + -
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Residues in contact with VAL 57 (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 VAL* 5.3 2.2 - - + +
16A LEU* 3.9 28.5 - - + +
17A PRO 3.6 17.3 - - - +
18A SER* 4.1 10.8 - - - +
19A TRP 4.4 0.7 - - - +
56A VAL* 1.3 84.5 - - - +
58A LEU* 1.3 69.9 + - - +
59A TRP* 4.5 0.4 - - + -
202A LYS* 3.8 26.9 - - + +
203A VAL 2.9 14.9 + - - +
204A VAL* 3.4 22.7 - - + -
205A PHE* 2.8 32.3 + - - +
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Residues in contact with LEU 58 (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 PRO* 4.7 7.5 + - - +
19A TRP* 5.3 9.9 - - + +
56A VAL* 4.9 1.0 - - - +
57A VAL* 1.3 75.1 - - - +
59A TRP* 1.3 64.5 + - - +
60A LYS 5.4 0.4 - - - +
205A PHE* 3.6 17.7 - - + +
207A VAL* 3.8 20.2 - - + -
212A GLU* 4.5 7.4 - - + +
215A TYR* 3.8 29.2 - - + -
216A GLN* 3.7 32.3 - - + +
219A LEU* 3.7 29.4 - - + -
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Residues in contact with TRP 59 (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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11A VAL* 3.9 31.6 - - + +
16A LEU* 3.8 33.4 - - + +
17A PRO* 6.3 0.9 - - + -
57A VAL* 4.5 2.2 - - + -
58A LEU* 1.3 76.6 - - - +
60A LYS* 1.3 73.0 + - - +
61A GLY* 3.4 20.3 + - - -
62A ASP 3.3 38.4 - - - -
63A VAL 4.1 0.7 - - - -
65A LEU* 4.4 4.5 - - + -
66A LEU* 3.7 33.0 - - + -
204A VAL* 4.0 15.0 - - + -
205A PHE 3.0 7.5 + - - -
206A ALA* 3.3 11.4 - - + -
207A VAL* 2.9 26.4 + - - -
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Residues in contact with LYS 60 (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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58A LEU* 4.3 0.6 - - - +
59A TRP* 1.3 84.9 + - - +
61A GLY* 1.3 57.3 + - - +
207A VAL* 3.3 17.4 - - + +
208A SER* 4.0 4.7 - - - -
209A ASP* 3.1 46.7 + - - +
212A GLU* 3.2 38.6 + - - +
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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