Contacts of the strand formed by residues 43 - 52 (chain A) in PDB entry 4C33
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 PHE 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ALA* 3.9 10.1 - - + -
39A HIS 3.4 22.7 - - - -
40A LEU* 3.2 21.1 + - + +
41A ASP* 3.3 2.3 - - - -
42A GLN* 1.3 81.8 - - + +
44A GLU* 1.3 60.8 + - - +
45A ARG 4.2 0.7 + - - -
60A VAL* 3.7 33.4 - - + -
61A LYS 3.3 5.4 - - - +
62A HIS* 3.4 40.8 - + + -
63A MET* 3.7 9.8 - - - +
69A TYR* 4.1 2.7 - + - -
71A MET* 5.0 7.4 - - + -
108A PHE* 3.9 19.5 - + - -
110A PHE* 3.9 19.7 - + - -
119A VAL* 4.0 23.8 - - + -
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Residues in contact with GLU 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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43A PHE* 1.3 73.3 - - - +
45A ARG* 1.3 70.0 + - - +
46A ILE* 3.6 20.6 + - + +
60A VAL* 3.2 7.6 - - - -
61A LYS* 2.8 50.7 + - + +
63A MET* 3.9 15.9 - - + +
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Residues in contact with ARG 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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43A PHE 4.1 1.4 + - - -
44A GLU* 1.3 77.5 - - - +
46A ILE* 1.3 68.6 + - - +
47A LYS 5.5 0.4 - - - +
48A THR* 3.8 1.2 + - - -
56A ARG* 4.6 0.2 - - - +
58A MET* 3.6 35.1 - - + +
59A LEU 4.2 2.7 - - - -
60A VAL* 4.4 6.5 - - + -
332A GLU* 2.8 33.9 + - - +
333A GLU 2.7 40.8 + - - +
334A GLU* 4.1 5.5 - - - +
335A ILE* 3.9 26.8 - - + +
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Residues in contact with ILE 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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44A GLU* 3.7 40.6 - - + +
45A ARG* 1.3 80.5 - - - +
47A LYS* 1.3 64.3 + - + +
59A LEU* 2.9 45.4 + - + +
60A VAL 4.1 2.7 - - - -
61A LYS* 4.0 20.6 - - + +
68A HIS* 4.5 7.9 - - + +
322A GLY 5.1 2.2 - - - +
324A THR* 5.4 1.1 - - + -
332A GLU* 5.6 0.9 - - - -
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Residues in contact with LYS 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 ILE* 1.3 87.9 - - + +
48A THR* 1.3 69.6 + - - +
49A LEU* 3.5 1.5 + - + +
58A MET* 3.5 9.3 - - - +
59A LEU* 2.7 34.7 + - + +
324A THR* 3.4 38.8 + - + +
327A PHE* 5.2 2.0 + - - +
328A ASP 3.9 6.7 + - - -
329A ASP* 2.8 42.3 + - - +
330A TYR 4.7 1.4 + - - +
332A GLU* 3.6 16.5 + - - +
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Residues in contact with THR 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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45A ARG* 3.8 4.3 + - - -
47A LYS* 1.3 82.2 + - - +
49A LEU* 1.3 58.7 + - - +
50A GLY 3.6 13.2 - - - +
51A THR* 3.2 27.1 - - - +
56A ARG* 4.9 10.1 - - + -
57A VAL 3.7 7.0 - - - +
58A MET* 3.4 14.5 - - - +
328A ASP 4.3 4.3 - - - +
330A TYR* 3.8 24.5 + - + +
331A GLU 4.4 7.4 + - - +
332A GLU* 2.7 36.6 + - - +
333A GLU 4.9 0.7 + - - -
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Residues in contact with LEU 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 LYS* 4.7 1.8 - - + +
48A THR* 1.3 74.2 - - - +
50A GLY* 1.3 54.0 + - - +
57A VAL* 2.7 29.3 + - + +
58A MET 4.1 3.6 - - - -
59A LEU* 3.6 32.3 - - + +
70A ALA* 4.3 4.0 - - + -
122A TYR* 3.6 29.4 - - + +
324A THR* 3.8 28.9 - - + -
327A PHE* 3.8 50.3 - - + +
330A TYR* 3.1 19.4 + - - -
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Residues in contact with GLY 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 THR* 3.5 3.2 - - - +
49A LEU* 1.3 79.9 - - - +
51A THR* 1.4 68.5 + - - -
55A GLY 4.8 0.4 - - - -
56A ARG* 3.3 1.9 - - - -
57A VAL* 2.9 35.6 + - - +
330A TYR* 3.8 12.9 - - - -
18I ARG* 6.1 3.4 - - - -
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Residues in contact with THR 51 (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 THR* 3.2 18.7 - - - +
50A GLY* 1.4 79.5 + - - -
52A GLY* 1.3 63.8 + - - +
55A GLY 3.6 6.7 - - - +
56A ARG* 3.7 20.9 - - + +
330A TYR* 4.3 24.6 - - - +
331A GLU 4.9 3.0 + - - +
333A GLU* 4.2 15.9 - - - +
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Residues in contact with GLY 52 (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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51A THR* 1.3 79.3 - - - +
53A SER* 1.4 65.6 + - - -
54A TYR 3.2 3.6 - - - -
55A GLY* 3.1 20.4 + - - +
20I ASN* 5.8 4.5 - - - -
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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