Contacts of the strand formed by residues 43 - 48 (chain A) in PDB entry 3UNF
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 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ILE 3.4 19.3 - - - +
38A LYS* 4.3 4.3 - - + -
42A GLY* 1.3 79.8 - - - +
44A VAL* 1.3 68.5 + - - +
136A CYS* 3.7 28.0 - - + -
137A GLY 4.2 5.6 - - - +
138A TRP* 5.9 0.2 - - + -
143A PRO* 3.6 18.8 - - + -
144A TYR 3.6 24.7 - - - +
145A LEU* 4.3 12.1 - - + -
183A LEU* 3.5 8.7 - - - +
211A ILE* 3.4 4.2 - - - -
212A CYS* 2.8 37.1 + - + +
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Residues in contact with VAL 44 (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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36A GLY* 3.3 4.0 - - - -
37A ILE* 3.0 42.0 + - + +
43A VAL* 1.3 74.0 - - - +
45A LEU* 1.3 69.0 + - - +
183A LEU* 4.4 3.8 - - + -
186A ALA* 3.4 37.5 - - + +
187A ILE* 3.8 27.8 - - + -
190A ALA* 3.9 12.3 - - + +
209A VAL* 3.8 20.4 - - + -
210A GLY 3.5 11.0 - - - +
211A ILE* 4.1 1.3 - - + -
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Residues in contact with LEU 45 (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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35A VAL 3.4 3.1 - - - +
36A GLY* 3.7 17.9 - - - -
43A VAL* 4.9 0.2 - - + -
44A VAL* 1.3 82.7 - - - +
46A ALA* 1.3 60.0 + - - +
64A VAL* 4.1 4.7 - - + +
72A GLY 4.2 8.5 - - - +
73A LEU 4.3 0.7 - - - +
74A VAL* 3.2 28.3 - - + -
134A LEU* 3.8 27.1 - - + +
136A CYS* 3.5 37.7 - - + +
145A LEU* 3.7 20.9 - - + -
208A GLU 4.1 0.2 - - - +
209A VAL* 3.2 2.9 - - - -
210A GLY 2.8 41.1 + - - +
217A PHE* 4.8 4.0 - - + -
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Residues in contact with ALA 46 (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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34A SER* 3.4 4.0 - - - -
35A VAL* 2.9 46.7 + - + +
44A VAL 4.3 0.4 - - - -
45A LEU* 1.3 73.7 - - - +
47A THR* 1.3 62.7 + - - +
74A VAL* 4.6 2.7 - - - +
190A ALA* 4.4 16.3 - - + +
191A ILE* 5.1 5.2 - - + -
194A LEU* 4.2 14.1 - - + -
207A ILE* 6.1 0.4 - - + -
208A GLU 3.3 8.7 - - - +
209A VAL* 4.0 14.6 - - + -
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Residues in contact with THR 47 (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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32A ALA 4.9 0.2 + - - -
33A PRO 3.4 7.2 + - - -
34A SER* 3.0 22.1 + - - -
46A ALA* 1.3 74.1 - - - +
48A GLU* 1.3 68.0 + - - +
63A LYS* 3.3 47.8 + - + -
64A VAL* 3.9 6.5 - - + -
74A VAL* 3.7 13.9 - - + -
194A LEU* 3.9 7.6 - - - -
207A ILE* 3.4 7.8 - - - +
208A GLU* 2.8 46.1 + - + +
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Residues in contact with GLU 48 (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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32A ALA* 3.7 14.6 - - - +
33A PRO* 3.2 40.2 + - + +
47A THR* 1.3 74.1 + - - +
49A LYS* 1.3 55.9 + - - +
50A LYS* 3.4 26.7 + - + +
63A LYS* 2.7 29.3 + - - -
164A LYS* 4.7 9.4 + - - +
194A LEU* 4.0 5.9 - - + +
197A SER 4.1 2.9 - - - +
198A PHE* 3.7 47.3 - - + +
206A ASN 4.1 1.6 - - - -
207A ILE* 4.6 4.3 - - - -
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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