Contacts of the strand formed by residues 41 - 54 (chain B) in PDB entry 3CMA
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 41 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLY* 1.3 73.8 - - - +
42B ALA* 1.3 88.2 + - - +
76B THR* 3.8 13.9 - - - -
77B PRO 3.3 24.5 - - - -
78B PRO* 3.7 7.9 - - - -
79B MET* 3.1 35.9 - - + -
162B MET* 4.7 1.6 - - - +
188B HIS* 3.9 18.6 - + - -
189B ALA* 3.6 22.9 - - - -
190B MET* 3.4 53.8 - - + -
193B ILE* 4.3 4.3 - - + -
194B PHE* 4.0 3.7 - - + -
310B ARG* 3.5 5.9 + - - +
311B PHE* 2.7 29.9 + + - +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 1.3 102.1 - - - +
43B GLY* 1.3 58.9 + - - +
76B THR* 4.1 5.1 - - - -
77B PRO* 4.6 2.3 - - - +
79B MET* 3.2 18.4 - - - +
146B THR* 4.2 3.4 - - + +
162B MET* 3.0 37.2 - - + -
308B LEU* 3.7 7.9 - - + -
309B VAL 3.4 12.6 - - - +
311B PHE* 4.1 2.7 - - - -
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Residues in contact with GLY 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA* 1.3 75.2 - - - +
44B TYR* 1.3 68.2 + - - -
74B ILE* 4.0 1.8 - - - -
75B GLU 3.2 14.1 - - - -
76B THR* 4.0 10.3 - - - -
77B PRO* 4.9 0.9 - - - -
308B LEU* 3.2 8.4 - - - +
309B VAL* 2.9 35.6 + - - -
311B PHE* 4.1 3.6 - - - -
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Residues in contact with TYR 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28370 U 5.9 0.2 - - - -
43B GLY* 1.3 76.7 - - - -
45B LYS* 1.3 66.3 + - - +
46B ALA 3.5 0.2 + - - -
74B ILE* 3.8 4.4 - - - +
75B GLU* 2.8 41.3 + - + +
77B PRO* 5.1 1.8 - - + -
146B THR* 2.7 31.7 + - + -
147B VAL 5.2 0.9 - - - -
148B PRO* 3.5 21.9 - - + +
151B VAL* 3.9 26.7 - - + -
154B VAL* 4.0 28.5 - - + -
156B LYS* 4.2 6.9 + - + -
160B ASP* 2.5 29.3 + - - -
287B TYR* 4.1 6.2 + - - +
306B LYS 3.3 22.4 - - - +
307B ARG 3.7 0.9 - - - -
308B LEU* 3.8 22.2 - - + -
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Residues in contact with LYS 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27170 C 2.8 30.3 + - - -
27180 C 3.0 12.8 + - - -
43B GLY 4.3 0.2 - - - -
44B TYR* 1.3 71.3 - - - +
46B ALA* 1.3 61.7 + - - +
47B GLY* 4.3 3.4 - - - +
48B MET* 5.5 2.7 - - - -
72B THR* 4.1 27.1 + - + +
73B VAL 4.2 3.4 - - - -
74B ILE* 4.2 7.4 - - + -
287B TYR* 3.1 10.6 - - - -
301B VAL* 3.1 21.9 + - + +
302B PRO 4.5 2.7 - - - +
303B GLY 2.9 20.3 + - - +
304B PRO 3.5 25.1 - - - +
305B ASP* 3.5 15.3 - - - +
306B LYS* 2.7 24.4 + - - +
307B ARG 3.2 15.1 + - - +
309B VAL* 4.3 10.3 - - + +
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Residues in contact with ALA 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TYR 3.5 2.4 + - - +
45B LYS* 1.3 75.1 - - - +
47B GLY* 1.3 62.2 - - - +
73B VAL* 3.1 20.9 + - + +
75B GLU* 4.5 2.0 - - + -
284B PHE* 3.7 9.8 - - + +
285B VAL 5.1 0.2 - - - +
287B TYR* 3.1 50.4 - - + +
290B VAL* 4.1 15.3 - - + -
305B ASP* 3.3 19.2 - - - +
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Residues in contact with GLY 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27190 A 5.6 1.3 - - - -
45B LYS* 4.3 2.7 - - - +
46B ALA* 1.3 82.3 - - - +
48B MET* 1.3 59.1 + - - -
72B THR* 3.2 8.1 - - - +
73B VAL 2.5 33.5 + - - -
284B PHE* 3.5 15.4 - - - -
305B ASP* 3.8 11.6 + - - -
335B ASN* 5.7 0.2 - - - -
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Residues in contact with MET 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27170 C 3.6 22.0 - - - +
27180 C 3.8 21.8 - - - +
27190 A 3.1 42.4 + - + +
45B LYS* 5.5 3.1 - - - -
47B GLY* 1.3 76.2 - - - -
49B THR* 1.3 72.9 + - - +
70B PRO* 4.1 12.6 - - + -
71B VAL 3.0 15.9 - - - +
72B THR* 3.3 19.1 - - + +
73B VAL* 4.4 1.3 - - - +
284B PHE* 3.9 3.6 - - - -
299B GLY 3.3 31.6 - - - +
300B SER* 4.4 2.0 - - - +
335B ASN* 3.0 21.0 + - - +
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Residues in contact with THR 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27190 A 3.3 16.8 - - - +
48B MET* 1.3 85.2 - - - +
50B HIS* 1.3 65.0 + - - +
71B VAL* 2.8 43.0 + - - +
73B VAL* 4.3 5.9 - - - +
278B PRO* 4.2 7.3 + - - +
280B VAL* 3.1 32.8 - - + -
284B PHE* 4.3 2.5 - - + -
330B VAL* 4.6 5.7 - - - +
331B SER* 3.7 24.9 + - - +
333B GLU 5.4 0.9 - - - +
335B ASN* 4.3 5.2 - - - +
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Residues in contact with HIS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27190 A 2.6 40.7 + - - +
27200 C 4.4 4.4 - - - -
49B THR* 1.3 81.3 + - - +
51B VAL* 1.3 65.6 - - - +
52B VAL* 5.4 1.1 - - + -
68B THR* 3.8 26.0 - - + -
69B VAL 3.2 12.1 - - - +
70B PRO* 4.4 0.4 - - - -
329B TYR* 4.6 6.5 - + - -
330B VAL* 4.0 0.9 - - - +
331B SER* 3.0 53.2 + - - -
333B GLU* 5.1 2.2 - - - -
14U GLU* 3.9 9.7 - - + +
15U PRO 2.7 29.5 + - - -
16U GLY 3.6 12.9 + - - -
17U THR* 4.3 3.4 - - - -
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B HIS* 1.3 76.9 - - - +
52B VAL* 1.3 61.1 + - - +
53B LEU* 3.2 19.5 - - + -
67B GLU 3.6 0.3 - - - +
68B THR* 3.5 1.4 - - - -
69B VAL* 2.7 45.5 + - + +
71B VAL* 4.1 24.5 - - + -
270B ILE* 4.4 3.8 - - + -
296B LEU* 5.1 6.3 - - + -
327B VAL* 3.2 25.8 - - + -
329B TYR* 2.7 23.3 - - - +
330B VAL* 3.4 16.2 - - + +
331B SER 4.7 0.2 - - - +
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B HIS* 5.4 2.5 - - + -
51B VAL* 1.3 74.8 - - - +
53B LEU* 1.3 67.8 + - - +
66B GLU* 3.9 26.9 - - + +
67B GLU 3.3 22.4 - - - +
68B THR* 4.6 13.9 - - + +
327B VAL* 3.5 0.7 - - - -
328B ARG* 2.8 29.5 + - + -
329B TYR* 2.9 45.4 + - + +
15U PRO* 4.8 11.2 - - + -
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B VAL* 3.2 33.2 - - + +
52B VAL* 1.3 79.5 - - - +
54B VAL* 1.3 68.4 + - - +
55B ASN* 3.5 1.1 + - - -
56B ASP* 6.4 0.4 - - + -
65B MET 3.5 0.2 - - - +
66B GLU* 3.3 4.2 - - - -
67B GLU* 2.7 41.6 + - + +
69B VAL* 4.4 15.3 - - + -
268B ARG* 4.4 8.1 - - - +
270B ILE* 3.6 33.0 - - + -
325B PRO* 4.3 14.1 - - + -
326B GLU 3.4 10.8 - - - +
327B VAL* 3.6 19.7 - - + -
328B ARG 5.3 0.4 - - - -
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 1.3 76.3 - - - +
55B ASN* 1.3 71.2 + - - +
56B ASP* 2.7 10.7 + - - +
64B GLY* 3.7 31.2 - - - +
65B MET 3.6 4.0 - - - -
66B GLU* 4.0 2.0 - - - +
325B PRO* 5.6 0.7 - - - +
326B GLU* 3.1 42.6 + - + +
328B ARG* 3.2 42.4 - - + +
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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