Contacts of the strand formed by residues 202 - 207 (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 LYS 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A VAL* 4.2 31.3 + - + -
14A ASP* 5.3 10.7 + - - +
16A LEU 5.0 7.1 + - - -
18A SER* 4.4 6.1 + - - -
54A GLY 3.3 21.8 - - - +
55A LYS* 3.2 11.9 - - - +
57A VAL* 3.8 16.6 - - + +
162A SER 3.2 2.8 + - - -
163A SER* 3.1 36.6 - - - -
164A VAL 3.1 4.7 + - - -
200A ILE* 3.7 4.3 - - - +
201A GLU* 1.3 92.2 - - + +
203A VAL* 1.3 66.5 + - - +
204A VAL* 4.1 0.7 - - + -
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Residues in contact with VAL 203 (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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55A LYS* 2.7 13.1 + - + +
56A VAL* 3.5 3.6 - - - +
57A VAL* 2.9 27.4 + - - +
153A LEU* 4.9 13.5 - - + -
164A VAL* 3.4 8.7 - - + +
166A PHE* 3.6 32.1 - - + -
189A VAL* 4.1 19.7 - - + -
193A LEU* 4.3 21.3 - - + -
200A ILE* 4.2 15.7 - - + -
202A LYS* 1.3 78.3 - - - +
204A VAL* 1.3 64.1 + - - +
205A PHE* 4.3 11.4 - - + -
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.7 28.9 - - + -
16A LEU* 4.6 4.7 - - + -
57A VAL* 3.4 21.1 - - + +
59A TRP* 4.0 26.0 - - + -
66A LEU* 3.9 19.7 - - + -
68A CYS* 4.0 11.4 - - - -
164A VAL 2.9 9.8 + - - +
165A GLY* 3.5 6.0 - - - -
166A PHE* 2.7 35.9 + - - +
202A LYS* 4.8 2.5 - - + -
203A VAL* 1.3 77.2 - - - +
205A PHE* 1.3 66.6 + - - +
206A ALA 4.0 0.4 - - - +
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Residues in contact with PHE 205 (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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56A VAL* 4.0 24.2 - - + -
57A VAL 2.8 18.6 + - - +
58A LEU* 3.6 10.6 - - + +
59A TRP 3.0 24.9 + - - +
149A TYR* 4.9 2.7 - + - -
166A PHE* 3.9 23.6 - + + -
167A CYS 5.8 0.7 - - - -
185A ALA* 4.5 10.8 - - + -
186A LEU* 3.7 29.8 - - + -
189A VAL* 3.6 42.6 - - + -
203A VAL* 4.3 9.4 - - + -
204A VAL* 1.3 72.3 - - - +
206A ALA* 1.3 62.2 + - - +
207A VAL* 4.3 1.1 - - + -
215A TYR* 3.8 33.7 - + + -
219A LEU* 4.9 3.4 - - + -
223A PHE* 5.0 1.3 - + - -
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Residues in contact with ALA 206 (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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59A TRP* 3.3 20.9 - - + -
61A GLY 3.9 13.2 - - - +
63A VAL* 3.8 27.8 - - + -
66A LEU* 4.4 3.8 - - + -
166A PHE 2.9 23.3 + - - +
167A CYS* 4.0 1.8 - - - -
168A VAL* 3.8 17.0 + - - +
204A VAL* 3.5 2.2 + - - +
205A PHE* 1.3 70.8 - - - +
207A VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 207 (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* 3.8 23.8 - - + -
59A TRP 2.9 16.8 + - - +
60A LYS* 3.3 12.8 - - - +
61A GLY* 3.0 28.5 + - - +
168A VAL* 4.1 6.5 - - + -
205A PHE* 4.0 3.8 - - + +
206A ALA* 1.3 80.1 - - - +
208A SER* 1.3 62.9 + - - +
211A GLU* 4.1 4.3 - - + +
212A GLU* 3.8 32.3 - - + +
215A TYR* 3.8 35.9 - - + -
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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