Contacts of the strand formed by residues 43 - 50 (chain A) in PDB entry 5A91
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 ARG 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 GLU* 3.4 3.6 - - - -
42A GLY* 1.3 72.3 - - - -
44A LEU* 1.3 60.9 + - - +
61A ARG* 3.7 20.2 - - - +
64A GLU* 3.1 30.8 + - - +
65A ARG 3.0 29.7 + - - -
66A PHE* 3.3 32.5 - - + +
174A PRO* 6.0 2.4 - - - +
175A GLY 5.8 4.6 - - - +
265A PHE* 3.3 7.4 - - - -
266A THR* 2.8 55.7 + - + +
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Residues in contact with LEU 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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33A LEU* 4.0 24.2 - - + +
36A LEU* 3.9 27.1 - - + -
37A GLU* 2.8 23.4 + - + +
43A ARG* 1.3 74.1 - - - +
45A GLY* 1.3 60.5 + - - +
46A VAL* 3.9 25.1 - - + -
60A TYR* 3.3 23.6 - - + -
61A ARG* 3.3 14.2 - - - +
66A PHE* 3.8 2.9 - - - -
263A THR* 5.3 0.4 - - - -
264A TYR 3.5 16.2 - - - +
265A PHE* 4.0 8.3 - - + -
278A ILE* 4.1 20.0 - - + -
279A LEU* 5.0 4.3 - - + -
282A ALA* 4.4 7.4 - - + -
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Residues in contact with GLY 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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44A LEU* 1.3 74.6 - - - +
46A VAL* 1.3 63.4 + - - +
60A TYR 3.3 7.2 - - - -
61A ARG* 4.3 0.2 - - - -
66A PHE* 3.5 24.4 - - - -
183A PRO* 3.8 9.3 - - - +
262A VAL 3.6 0.5 - - - +
263A THR* 3.4 4.3 - - - -
264A TYR* 2.8 40.3 + - - +
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Residues in contact with VAL 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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33A LEU* 4.4 9.0 - - + -
44A LEU* 3.9 28.7 - - + -
45A GLY* 1.3 80.4 - - - +
47A ALA* 1.3 69.0 + - - +
48A LEU 4.4 0.4 - - - +
57A ILE 4.3 6.1 - - - +
59A LEU* 3.4 3.1 - - - -
60A TYR* 2.8 43.7 + - + +
62A ALA* 3.5 3.6 - - - +
183A PRO* 4.0 3.8 - - - +
261A LEU* 3.9 22.9 - - + -
262A VAL 3.3 3.1 - - - +
263A THR* 4.4 5.6 - - + -
282A ALA* 4.2 14.1 - - + -
286A VAL* 4.1 21.5 - - + -
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Residues in contact with ALA 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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46A VAL* 1.3 75.8 - - - +
48A LEU* 1.3 59.8 + - - +
49A ILE* 5.7 0.2 - - + -
57A ILE 3.4 5.2 - - - -
59A LEU* 3.9 12.3 - - + -
62A ALA* 4.2 0.2 - - + -
183A PRO* 3.5 32.2 - - - +
184A LEU* 3.7 12.6 - - + +
187A ALA* 3.9 10.1 - - + +
260A VAL 3.6 1.4 - - - +
261A LEU* 3.4 4.4 - - - -
262A VAL* 2.8 36.2 + - + -
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Residues in contact with LEU 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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46A VAL* 4.4 0.4 - - + +
47A ALA* 1.3 73.2 - - - +
49A ILE* 1.3 78.0 + - - +
50A ASN* 3.7 15.0 - - + +
55A SER 4.9 0.7 - - - +
56A GLN* 3.1 9.9 - - - +
57A ILE* 2.9 58.6 + - + +
59A LEU* 4.7 0.3 - - - +
259A LEU* 4.3 18.2 - - + -
260A VAL 3.2 7.9 - - - +
261A LEU* 4.0 15.0 - - + -
286A VAL* 3.7 35.4 - - + +
287A THR* 4.0 15.0 - - + -
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Residues in contact with ILE 49 (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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47A ALA* 5.4 0.4 - - + -
48A LEU* 1.3 78.5 - - - +
50A ASN* 1.3 68.8 + - - +
51A THR* 3.6 5.4 + - + +
54A ASN* 4.8 8.7 - - - +
55A SER 3.6 7.9 - - - +
56A GLN* 4.3 19.7 - - + +
184A LEU* 4.9 3.6 - - + -
187A ALA* 3.7 42.2 - - + +
188A GLN* 3.8 19.5 - - + +
191A LYS* 4.1 27.4 - - + +
259A LEU* 3.3 5.0 - - - -
260A VAL* 2.8 40.0 + - + +
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Residues in contact with ASN 50 (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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48A LEU* 3.7 9.7 - - + +
49A ILE* 1.3 71.1 - - - +
51A THR* 1.3 58.2 + - - +
52A ALA* 2.9 27.2 + - - +
53A ASP* 3.5 16.7 + - - -
54A ASN* 2.8 27.5 + - - -
55A SER* 2.8 25.9 + - - +
257A ALA 4.7 1.6 - - - +
258A PRO 4.3 0.7 - - - +
259A LEU* 3.7 24.6 - - + +
290A PHE* 4.6 12.7 - - - -
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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