Contacts of the strand formed by residues 42 - 48 (chain A) in PDB entry 2I6D
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 CYS 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.8 16.6 - - + -
40A TYR 3.4 4.2 + - - +
41A ARG* 1.3 94.8 + - - +
43A ARG* 1.3 56.5 + - - +
44A MSE 3.3 31.0 - - - -
45A LEU* 4.2 4.0 - - - -
58A PRO* 3.8 29.2 - - + -
59A HIS 4.4 2.8 - - - +
61A ALA* 3.4 11.9 - - - +
86A ALA* 4.5 4.3 - - - -
87A VAL 3.5 6.3 - - - -
88A PHE* 3.6 18.8 - - + -
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Residues in contact with ARG 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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9A PHE* 3.3 25.9 - - + -
22A GLU* 2.7 52.9 + - - -
23A GLN 4.5 1.4 + - - -
24A ALA* 3.6 11.6 - - - +
41A ARG* 3.6 8.4 + - - +
42A CYS* 1.3 73.0 - - - +
44A MSE 1.3 65.0 + - + +
60A ASP 4.8 0.6 - - - +
61A ALA* 3.6 4.9 - - - -
62A GLU* 3.0 22.3 + - - +
87A VAL* 2.8 26.6 + - + +
88A PHE* 5.0 0.4 - - - +
89A ASP* 4.1 20.0 + - - +
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Residues in contact with MSE 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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6A GLN* 3.3 42.4 - - + +
9A PHE* 4.3 16.4 - - + -
10A LEU* 4.1 33.2 - - + -
42A CYS* 3.3 9.8 - - - -
43A ARG* 1.3 86.1 - - + +
45A LEU* 1.3 64.1 + - - +
46A VAL* 3.8 14.8 - - + -
62A GLU* 3.1 31.4 - - + +
64A VAL* 4.6 5.2 - - + -
85A MSE 5.4 0.4 - - - +
86A ALA* 3.4 0.7 - - - -
87A VAL* 2.7 44.1 + - + -
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Residues in contact with LEU 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 VAL* 3.9 11.7 - - + -
37A LEU* 5.1 2.9 - - + -
42A CYS* 4.2 9.4 - - - -
44A MSE 1.3 75.0 - - - +
46A VAL* 1.3 62.1 + - - +
52A LEU* 3.7 23.3 - - + -
55A VAL* 3.9 18.6 - - + -
57A THR* 5.4 0.9 - - + -
58A PRO* 3.7 27.8 - - + -
62A GLU 2.8 9.3 + - - +
63A VAL* 3.2 16.6 - - + +
64A VAL 2.9 24.9 + - - +
84A LEU* 3.9 18.8 - - + -
85A MSE 3.7 4.3 - - - +
86A ALA* 3.7 25.6 - - + -
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Residues in contact with VAL 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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2A LEU* 4.0 28.3 - - + -
10A LEU* 4.4 6.5 - - + -
44A MSE 3.8 23.3 - - + -
45A LEU* 1.3 79.4 - - - +
47A GLY* 1.3 58.4 + - - +
64A VAL* 3.4 11.7 - - + +
66A LEU* 3.2 35.0 - - + -
72A PHE* 4.2 2.6 - - + -
75A ILE* 4.2 13.0 - - + -
84A LEU* 3.3 6.2 - - - +
85A MSE 2.9 41.2 + - + +
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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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46A VAL* 1.3 77.4 - - - +
48A THR* 1.3 66.6 + - - -
52A LEU* 3.6 6.5 - - - +
64A VAL 3.1 7.1 + - - +
65A GLU* 3.3 6.6 - - - -
66A LEU* 2.8 26.4 + - - -
72A PHE* 4.0 5.4 - - - -
83A PRO 3.2 14.1 - - - -
84A LEU* 4.0 10.5 - - - -
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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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47A GLY* 1.3 74.4 - - - -
49A ALA* 1.3 66.6 + - - +
50A ALA* 4.0 5.8 + - - +
51A MSE 2.9 35.5 + - - +
52A LEU* 2.9 12.3 + - - +
66A LEU 3.4 16.8 - - - +
67A PRO 4.0 11.7 - - - +
68A GLU* 3.9 31.8 + - - +
72A PHE* 4.3 8.3 - - + -
83A PRO* 3.2 24.0 + - + +
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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