Contacts of the helix formed by residues 32 - 45 (chain A) in PDB entry 1BY7
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 PRO 32 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ASN* 3.0 18.0 - - - +
11A PHE* 4.4 5.5 - - + -
12A ALA* 3.4 38.4 - - + -
15A LEU* 5.3 0.7 - - + -
30A LEU* 3.3 28.9 - - + +
31A SER* 1.3 84.0 - - - +
33A TRP* 1.3 57.0 + - - +
35A ILE* 3.1 8.3 + - + +
36A SER* 2.8 27.7 + - - -
406A ILE* 4.1 12.1 - - + -
407A LEU 3.5 11.0 - - - +
408A PHE* 3.7 7.9 - - - -
409A PHE* 3.8 6.3 - - + +
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Residues in contact with TRP 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASN* 3.2 14.9 + - - +
31A SER* 3.2 10.0 - - - -
32A PRO* 1.3 78.2 - - - +
34A SER* 1.3 82.4 + - - +
36A SER* 3.4 2.8 + - - -
37A SER* 3.0 29.5 + - - -
107A PHE* 5.0 7.6 - + - -
110A LEU* 5.8 1.9 - - + +
111A SER* 5.4 8.7 - - - +
114A ILE* 3.5 39.7 - - + +
115A ASN* 4.4 17.7 - - - -
123A LEU* 4.2 35.4 - - + -
125A SER* 4.4 15.3 - - - -
202A VAL* 4.4 9.9 - - + -
405A CYS* 4.8 7.9 - - - -
406A ILE 3.5 18.4 + - - +
407A LEU* 3.8 22.0 - - + -
408A PHE* 5.6 0.2 - + - -
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Residues in contact with SER 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A SER* 3.2 21.7 + - - -
33A TRP* 1.3 91.0 - - - +
35A ILE* 1.3 52.9 + - - +
37A SER* 4.0 4.4 - - - +
38A THR* 2.8 41.5 + - - +
125A SER* 3.9 8.1 - - - -
200A ASN* 2.6 32.8 + - - -
202A VAL* 3.3 18.1 - - - +
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Residues in contact with ILE 35 (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 PHE* 3.7 24.0 - - + -
15A LEU* 3.8 24.7 - - + -
30A LEU* 4.4 4.3 - - + -
31A SER 3.2 19.1 - - - +
32A PRO* 3.1 5.3 + - + +
34A SER* 1.3 73.2 + - - +
36A SER* 1.4 68.2 + - - +
38A THR* 3.7 5.2 - - - -
39A MET* 2.8 44.3 + - + +
200A ASN* 4.2 1.6 - - - +
320A LEU* 4.0 20.9 - - + -
324A LEU* 5.5 2.7 - - + -
354A VAL* 5.7 3.6 - - + -
356A HIS* 3.6 37.0 - - + +
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Residues in contact with SER 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASN* 2.6 38.8 + - - +
11A PHE* 3.5 16.3 - - - +
32A PRO 2.8 8.9 + - - -
33A TRP 3.7 3.8 - - - -
34A SER 3.3 0.2 - - - -
35A ILE* 1.4 78.3 - - - +
37A SER* 1.3 56.4 + - - +
39A MET* 3.8 0.9 - - - +
40A ALA* 2.8 30.1 + - - +
58A LEU* 4.4 17.6 + - - +
60A PHE* 4.7 4.4 - - - -
107A PHE* 3.8 16.5 - - - -
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Residues in contact with SER 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 3.0 25.5 + - - -
34A SER* 4.0 5.8 - - - -
36A SER* 1.3 72.8 - - - +
38A THR* 1.3 69.6 + - - +
40A ALA* 3.3 1.2 + - - +
41A MET 3.1 16.8 + - - -
107A PHE* 3.6 24.4 - - - +
111A SER* 6.2 0.5 - - - -
149A TYR* 3.3 29.2 - - - -
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Residues in contact with THR 38 (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* 2.8 26.1 + - - +
35A ILE* 3.4 8.3 + - - -
37A SER* 1.3 79.1 - - - +
39A MET* 1.3 62.2 + - - +
41A MET* 3.2 19.7 + - - +
42A VAL* 3.4 15.6 + - - +
125A SER* 6.0 0.2 - - - +
127A ASN* 3.5 42.8 - - + +
149A TYR* 5.5 0.7 - - - -
198A LEU* 3.7 25.9 - - + +
200A ASN* 4.2 15.3 + - + +
354A VAL* 5.9 0.7 - - - +
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Residues in contact with MET 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 5.4 0.7 - - + -
35A ILE* 2.8 44.9 + - + +
36A SER 4.0 0.4 - - - +
38A THR* 1.3 68.4 + - - +
40A ALA* 1.3 58.8 + - - +
42A VAL* 3.2 7.9 + - + +
43A TYR* 3.0 27.5 + - - +
54A MET* 3.5 15.3 - - + +
58A LEU* 4.0 24.2 - - + -
198A LEU* 3.9 20.2 - - - -
324A LEU* 3.9 15.7 - - + -
329A MET* 3.5 33.0 - - + -
351A LEU* 4.2 17.3 - - + -
354A VAL* 3.9 15.3 - - - -
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Residues in contact with ALA 40 (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 SER 2.8 14.1 + - - +
37A SER 3.4 4.7 - - - +
39A MET* 1.3 76.6 - - - +
41A MET* 1.3 56.6 + - - +
43A TYR* 3.2 10.5 + - - +
44A MET 2.9 24.1 + - - -
58A LEU* 4.1 4.9 - - - +
60A PHE* 4.1 7.0 - - + -
103A ILE* 4.6 2.2 - - + -
104A HIS* 3.4 7.6 + - - -
107A PHE* 3.2 35.4 - - + -
149A TYR* 3.2 13.2 - - - +
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Residues in contact with MET 41 (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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37A SER 3.1 8.0 + - - +
38A THR* 3.2 16.5 + - - +
40A ALA* 1.3 75.2 - - - +
42A VAL* 1.3 59.0 + - + +
44A MET* 3.3 16.6 - - + +
127A ASN* 4.7 4.7 - - - +
129A LEU* 4.0 29.2 - - + +
141A TYR* 2.7 30.0 + - - +
145A CYS* 3.6 26.2 - - - -
149A TYR* 3.5 39.6 - - + -
151A SER* 3.8 33.7 - - - +
153A PRO* 5.3 2.5 - - + -
198A LEU* 4.7 9.4 - - + -
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Residues in contact with VAL 42 (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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38A THR 3.7 11.4 - - - +
39A MET* 3.2 11.6 + - + +
41A MET* 1.3 75.3 - - + +
43A TYR* 1.3 59.8 + - - +
45A GLY* 2.9 23.7 + - - -
46A SER 3.5 3.3 + - - -
54A MET* 4.0 11.9 - - + -
129A LEU* 4.2 26.5 - - + -
141A TYR* 3.8 0.2 - - - -
196A MET* 4.9 2.5 - - + -
198A LEU* 4.2 18.4 - - + -
340A PHE* 3.5 29.4 - - + -
343A MET* 3.6 15.6 - - + +
351A LEU* 4.4 15.3 - - + -
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Residues in contact with TYR 43 (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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39A MET 3.0 13.7 + - - +
40A ALA* 3.4 12.6 - - - +
42A VAL* 1.3 76.3 - - - +
44A MET* 1.3 58.8 + - - +
46A SER* 2.8 38.7 + - - +
47A ARG* 4.8 0.2 + - - -
51A GLU* 3.5 46.1 + - + +
54A MET* 3.7 24.0 - - + +
55A ALA* 3.7 20.8 - - + +
58A LEU* 4.6 2.0 - - + -
60A PHE* 3.9 16.4 - + - -
100A ALA* 4.4 12.2 + - - +
103A ILE* 3.5 31.9 - - + +
104A HIS* 3.8 18.8 - + - -
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Residues in contact with MET 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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40A ALA 2.9 8.5 + - - +
41A MET 3.3 7.6 - - - +
42A VAL 3.2 0.4 - - - -
43A TYR* 1.3 75.3 - - - +
45A GLY* 1.4 56.3 + - - +
47A ARG* 2.8 21.7 + - - -
104A HIS* 3.3 52.7 - - + +
141A TYR* 4.0 16.7 - - + -
144A LEU* 3.5 55.3 - - + +
145A CYS* 3.7 11.7 - - - +
148A TYR* 4.2 6.5 - - - -
149A TYR* 4.0 14.6 - - + -
342A GLY* 4.9 0.3 - - - -
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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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41A MET 3.6 3.8 + - - -
42A VAL 2.9 12.2 + - - -
44A MET* 1.4 77.6 - - - +
46A SER* 1.3 56.4 + - - +
47A ARG* 3.7 2.7 - - - -
141A TYR* 3.6 9.0 - - - -
340A PHE* 3.3 12.6 - - - -
342A GLY* 3.1 23.6 + - - -
343A MET* 3.2 28.5 + - - -
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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
------------------------------------------------------------
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