Contacts of the strand formed by residues 27 - 34 (chain A) in PDB entry 4ICX
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 MSE 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A PRO 5.7 2.0 - - - +
25A LYS 5.7 0.9 - - - -
26A HIS* 1.3 100.8 - - - +
28A LEU* 1.3 63.9 + - - +
43A PRO* 3.9 25.6 - - + +
44A VAL* 3.2 19.1 - - - +
45A ASP* 3.1 42.8 - - - +
46A HIS* 3.9 6.2 - - - +
81A ALA* 3.4 6.6 - - - +
82A LEU* 2.8 38.7 + - + +
84A PRO* 3.6 26.5 - - + -
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Residues in contact with LEU 28 (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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20A PHE* 3.7 23.8 - - + -
27A MSE 1.3 71.0 - - - +
29A VAL* 1.3 62.5 + - - +
42A ASP 3.7 1.6 - - - +
43A PRO* 3.2 4.0 - - - +
44A VAL* 2.7 42.0 + - + +
46A HIS* 3.4 38.4 - - + +
50A PRO* 3.6 33.7 - - + -
52A PHE* 4.0 17.6 - - + -
79A CYS* 3.9 16.8 - - - -
80A PHE 3.3 19.1 - - - +
81A ALA* 4.2 1.6 - - + +
92A ILE* 4.6 4.3 - - + -
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Residues in contact with VAL 29 (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 LEU* 1.3 80.7 - - - +
30A VAL* 1.3 72.9 + - - +
31A GLU* 4.1 11.0 - - + +
40A ALA* 4.5 8.7 - - + -
41A THR* 3.8 23.3 - - - +
43A PRO* 3.7 25.1 - - + -
79A CYS* 3.6 2.5 - - - -
80A PHE* 2.8 45.3 + - + +
82A LEU* 4.2 21.3 - - + -
89A LYS* 5.5 5.8 - - + -
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Residues in contact with VAL 30 (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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14A ILE* 3.9 22.9 - - + -
29A VAL* 1.3 74.4 - - - +
31A GLU* 1.3 75.3 + - - +
32A ALA* 5.2 0.4 - - + -
40A ALA* 3.4 2.4 - - - +
41A THR* 3.0 43.0 + - + +
52A PHE* 3.7 31.1 - - + -
56A LEU* 4.9 1.0 - - - +
77A LEU* 4.0 20.6 - - + -
78A GLN 3.3 6.7 - - - +
79A CYS* 4.2 9.4 - - + -
126A ILE* 4.1 16.8 - - + -
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Residues in contact with GLU 31 (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 VAL* 4.1 6.5 - - + +
30A VAL* 1.3 76.9 - - - +
32A ALA* 1.3 60.4 + - - +
38A GLN* 2.9 36.2 + - + +
39A LEU 3.2 5.8 - - - +
40A ALA* 3.9 19.1 - - + +
76A LYS 3.8 0.2 - - - +
77A LEU* 3.3 3.1 - - - -
78A GLN* 2.8 41.1 + - + +
80A PHE* 3.4 29.5 - - + -
89A LYS* 2.7 30.7 + - - -
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Residues in contact with ALA 32 (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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12A VAL* 6.0 0.7 - - + -
30A VAL* 5.2 0.2 - - + -
31A GLU* 1.3 75.1 - - - +
33A LYS* 1.3 61.4 + - - +
37A GLU 3.6 1.7 - - - +
38A GLN* 3.3 3.7 - - - -
39A LEU 2.7 39.3 + - - +
56A LEU* 3.8 17.9 - - + +
58A TRP* 3.6 27.1 - - + -
75A ILE* 4.7 0.9 - - + -
76A LYS 3.3 7.4 - - - +
77A LEU* 4.0 19.3 - - + -
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Residues in contact with LYS 33 (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 ALA* 1.3 74.4 - - - +
34A PHE* 1.3 62.7 + - - +
35A ASP 4.3 0.2 - - - -
36A GLY* 4.1 26.1 + - - +
37A GLU 3.4 14.4 - - - +
38A GLN* 4.5 24.7 + - + +
58A TRP* 4.5 0.7 - - - -
74A PRO 3.9 2.4 - - - +
75A ILE* 3.8 1.5 - - - +
76A LYS* 2.9 43.6 + - + +
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Residues in contact with PHE 34 (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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10A ILE* 3.6 26.2 - - + -
33A LYS* 1.3 74.0 - - - +
35A ASP* 1.3 81.0 + - + +
36A GLY 3.2 0.9 - - - -
37A GLU* 3.1 24.7 + - - +
58A TRP* 3.8 38.6 - + + +
59A GLU 5.5 1.1 - - - -
60A ILE* 4.1 13.7 - - + -
68A HIS* 3.6 27.1 - + - -
73A THR* 3.9 26.7 - - + -
74A PRO 3.7 15.7 - - - -
75A ILE* 3.8 20.9 - - + -
99A LEU* 4.3 12.3 - - + -
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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