Contacts of the strand formed by residues 43 - 50 (chain A) in PDB entry 3M2K
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 LYS 43 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLU* 3.2 10.3 - - - +
42A ALA* 1.3 78.8 - - - +
44A LEU* 1.3 64.9 + - - +
61A ARG* 3.7 21.8 - - - +
64A GLU* 2.5 31.0 + - - +
65A ARG 4.8 4.2 + - - -
66A PHE* 3.7 22.7 - - + -
265A SER* 2.9 31.0 - - - -
266A SER* 2.9 19.3 + - - +
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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
----------------------------------------------------------
33A PHE* 3.6 43.7 - - + +
36A LEU* 4.5 4.5 - - + -
37A GLU* 3.1 14.6 + - + +
42A ALA 4.0 0.2 + - - -
43A LYS* 1.3 76.8 - - - +
45A GLY* 1.4 56.6 + - - +
46A ILE* 3.6 17.0 - - + -
60A TYR* 3.4 25.3 - - + -
61A ARG* 3.5 12.3 - - - -
66A PHE* 3.7 4.3 - - - -
263A VAL* 4.9 4.3 - - + -
264A LEU 3.1 9.6 - - - +
265A SER* 4.2 1.6 - - - -
278A LEU* 4.0 41.5 - - + -
282A ALA* 4.4 11.7 - - + -
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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* 1.4 68.1 - - - +
46A ILE* 1.4 63.3 + - - +
60A TYR 3.8 2.9 - - - -
61A ARG 4.0 6.5 - - - -
66A PHE* 3.1 28.9 - - - -
183A ALA* 4.0 9.9 - - - +
262A ALA 3.6 1.4 - - - +
263A VAL* 3.4 2.1 - - - -
264A LEU* 2.5 42.9 + - - +
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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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33A PHE* 3.4 38.4 - - + -
44A LEU* 3.6 22.9 - - + -
45A GLY* 1.4 76.1 - - - +
47A PHE* 1.3 67.0 + - - +
57A VAL* 4.5 9.4 - - + +
59A ALA* 3.2 2.1 - - - -
60A TYR* 2.4 55.3 + - + +
61A ARG 4.2 0.6 + - - -
62A PRO* 3.9 3.2 - - - +
183A ALA* 3.9 4.7 - - - +
261A LEU* 4.6 1.3 - - + -
262A ALA 3.5 11.0 - - - +
263A VAL* 4.2 13.0 - - + -
282A ALA* 4.6 7.4 - - + -
286A VAL* 3.7 26.2 - - + -
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Residues in contact with PHE 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 72.4 - - - +
48A ALA* 1.3 65.6 + - - +
49A LEU* 3.6 31.9 - - + -
56A THR* 3.7 22.7 - - + -
57A VAL 3.2 11.0 - - - -
59A ALA* 4.5 5.4 - - + -
62A PRO* 4.0 20.4 - - + -
183A ALA* 3.8 3.3 - - + +
184A ARG* 3.8 56.8 - - - +
187A VAL* 3.4 25.0 - - + +
188A THR* 5.2 5.2 - - - -
261A LEU* 3.3 3.2 - - - +
262A ALA 2.9 31.2 + - - -
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Residues in contact with ALA 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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47A PHE* 1.3 82.0 - - - +
49A LEU* 1.3 64.6 + - - +
56A THR* 3.4 3.8 - - - -
57A VAL* 3.0 34.9 + - + +
259A VAL* 4.4 9.9 - - + -
260A VAL 3.4 7.4 - - - +
261A LEU* 3.9 4.7 - - + -
286A VAL* 3.5 33.4 - - + -
290A LEU* 4.6 5.2 - - + -
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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 PHE* 3.6 22.0 - - + -
48A ALA* 1.3 78.3 - - - +
50A ASP* 1.3 76.1 + - - +
51A THR* 3.7 4.5 + - + +
54A ASN* 3.8 21.8 - - - +
55A ARG 3.3 12.6 - - - +
56A THR* 4.4 4.9 - - - +
187A VAL* 4.4 10.3 - - + -
188A THR* 5.7 3.6 - - - +
191A ARG* 3.9 28.0 - - - +
259A VAL* 2.9 18.2 - - - +
260A VAL* 2.8 25.2 + - + +
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Residues in contact with ASP 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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49A LEU* 1.3 71.5 - - - +
51A THR* 1.3 57.2 + - - +
52A GLY* 3.3 11.1 + - - -
53A THR* 3.5 16.9 + - - +
54A ASN* 2.5 37.4 + - - -
55A ARG* 2.8 44.9 + - - +
257A ASP 4.1 6.4 - - - +
258A PRO 3.9 2.6 - - - +
259A VAL* 3.5 26.2 - - + +
290A LEU* 4.3 10.7 - - + +
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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