Contacts of the strand formed by residues 40 - 50 (chain A) in PDB entry 1BMA
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 SER 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ARG* 3.4 11.4 - - - +
37A SER* 2.8 41.7 + - - -
39A SER* 1.3 83.0 + - - +
41A TRP* 1.3 67.7 + - - +
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Residues in contact with TRP 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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34A GLN* 3.7 20.5 - - + +
35A TYR* 3.3 28.7 - - - -
36A ARG* 3.3 33.4 - - + +
37A SER* 4.8 0.9 - - - -
39A SER 5.0 3.4 + - - -
40A SER* 1.3 86.5 - - - +
42A ALA* 1.3 57.8 + - - +
67A THR* 3.5 32.8 - - + -
68A PHE 4.6 0.9 - - - -
69A ARG* 3.6 68.6 - - + +
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Residues in contact with ALA 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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34A GLN* 3.1 5.5 - - - -
35A TYR* 3.0 57.8 + - + +
37A SER* 4.3 10.9 - - - +
41A TRP* 1.3 73.5 - - - +
43A HIS* 1.3 65.7 + - - +
44A THR 3.5 0.3 + - - -
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Residues in contact with HIS 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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32A SER* 2.9 24.5 + - - +
33A LEU 3.9 4.5 + - - -
34A GLN* 4.1 7.7 - - - +
35A TYR* 4.6 1.6 - - - -
42A ALA* 1.3 75.8 - - - +
44A THR* 1.3 60.1 + - - +
45A CYS 3.1 28.7 + - - -
46A GLY 4.2 0.9 - - - -
77A LEU* 3.9 24.8 - - + +
147A TRP* 3.8 34.4 - + + +
156A LEU* 4.2 35.7 - - + +
201A GLY 2.9 25.6 + - - -
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Residues in contact with THR 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* 3.0 25.2 + - + +
34A GLN 4.6 0.4 - - - +
35A TYR* 3.6 30.5 - - + -
42A ALA 3.5 0.4 + - - -
43A HIS* 1.3 78.9 - - - +
45A CYS* 1.3 79.0 + - + +
61A CYS 4.8 4.0 + - - +
66A LEU* 5.9 0.8 - - + +
68A PHE* 4.3 19.3 - - + -
201A GLY* 3.6 18.2 + - - -
203A SER* 5.0 0.2 - - - -
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Residues in contact with CYS 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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33A LEU* 2.8 37.8 + - + -
43A HIS* 3.1 16.5 + - - -
44A THR* 1.3 93.5 - - - +
46A GLY* 1.3 65.7 + - - +
60A HIS* 5.0 1.6 - - - -
61A CYS* 2.0 55.4 - - + -
201A GLY 3.9 4.5 - - - -
203A SER* 3.4 14.8 - - - +
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Residues in contact with GLY 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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30A GLN* 3.7 10.8 - - - -
31A ILE* 3.4 18.4 - - - +
33A LEU* 4.6 0.7 - - - +
43A HIS* 4.6 3.6 - - - -
45A CYS* 1.3 77.1 - - - +
47A GLY* 1.3 56.7 + - - -
57A THR* 2.9 20.8 + - - -
146A GLY* 6.3 1.6 - - - -
147A TRP* 5.5 0.2 - - - -
201A GLY 4.0 5.8 + - - -
202A ASP* 4.2 2.0 + - - -
203A SER 2.9 11.7 + - - +
204A GLY 3.3 10.6 - - - -
205A GLY* 4.0 4.9 - - - -
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Residues in contact with GLY 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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30A GLN* 3.7 9.8 + - - +
31A ILE* 3.1 39.5 + - - +
46A GLY* 1.3 74.4 - - - -
48A THR* 1.3 63.9 + - - -
55A VAL* 4.6 0.2 - - - -
56A MET 3.3 13.5 - - - -
57A THR* 4.2 2.0 - - - -
204A GLY 3.4 7.4 - - - -
205A GLY* 3.7 2.8 - - - -
206A PRO* 3.8 4.6 - - - +
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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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29A SER* 3.4 22.0 - - - +
31A ILE* 4.1 0.8 - - - +
47A GLY* 1.3 75.3 - - - -
49A LEU* 1.3 73.9 + - - +
50A ILE* 3.3 9.8 + - + +
55A VAL* 3.4 4.6 - - - -
56A MET* 2.9 46.9 + - + +
127A GLY* 4.1 4.5 - - - -
129A LEU* 5.6 0.4 - - + -
204A GLY 5.0 0.7 + - - -
205A GLY 4.6 0.9 - - - -
206A PRO* 3.4 25.5 - - - +
217A VAL* 3.8 25.5 - - + +
220A VAL* 5.9 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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28A PRO 5.2 1.1 - - - +
29A SER* 2.9 18.8 + - - +
31A ILE* 3.9 8.7 - - + +
48A THR* 1.3 69.2 - - - +
50A ILE* 1.3 57.6 + - - +
51A ARG 3.2 22.0 - - - +
54A TRP 3.8 7.4 - - - +
55A VAL* 4.0 14.6 - - + -
72A VAL* 4.5 11.0 - - + -
114A LEU* 4.5 8.1 - - + -
118A VAL* 3.9 19.3 - - + -
120A LEU* 4.1 2.0 - - + -
124A VAL* 3.8 29.6 - - + -
125A GLN 3.8 16.2 - - - +
126A LEU* 3.6 15.2 - - + -
127A GLY* 2.8 27.9 + - - -
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Residues in contact with ILE 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* 3.3 16.3 + - + +
49A LEU* 1.3 77.4 - - - +
51A ARG* 1.3 90.0 + - + +
54A TRP* 3.0 23.4 + - + +
55A VAL 4.4 0.9 - - - +
56A MET* 4.1 15.5 - - + +
111A LEU* 3.8 29.4 - - + -
126A LEU* 3.7 15.8 - - - +
127A GLY 4.5 8.9 - - - +
129A LEU* 4.1 28.9 - - + -
248A ILE* 4.1 9.6 - - + -
252A ILE* 4.0 21.1 - - + -
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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