Contacts of the strand formed by residues 23 - 31 (chain A) in PDB entry 4CYM
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 GLU 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ARG* 1.3 81.3 - - - +
24A HIS* 1.3 67.7 + - - +
74A LEU* 3.2 25.6 - - + +
76A ARG* 3.0 31.0 + - - -
554D GLU* 4.3 16.1 - - - +
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Residues in contact with HIS 24 (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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22A ARG* 3.9 41.7 + - + -
23A GLU* 1.3 78.7 - - - +
25A LEU* 1.3 56.9 + - - +
26A PHE* 3.6 35.7 - + + -
73A THR* 4.7 12.2 - - + -
74A LEU 2.9 16.2 + - - +
75A VAL* 4.4 6.6 - - + +
76A ARG* 2.6 37.7 + - - +
193A LEU* 3.8 23.9 - - + +
196A HIS* 5.4 11.9 + + + +
197A GLN* 5.5 1.8 + - - +
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Residues in contact with LEU 25 (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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24A HIS* 1.3 74.2 - - - +
26A PHE* 1.3 69.5 + - - +
27A LYS 4.3 0.5 + - - -
64A LEU* 4.9 3.4 - - + -
76A ARG* 3.4 35.2 - - + -
78A GLN* 3.9 26.0 - - + +
100A VAL* 5.9 0.7 - - - +
553D VAL* 2.9 55.8 - - + +
554D GLU* 4.5 19.1 - - + +
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Residues in contact with PHE 26 (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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24A HIS* 3.6 38.6 - + + -
25A LEU* 1.3 78.7 - - - +
27A LYS* 1.3 59.2 + - - +
28A VAL* 3.5 5.1 + - + +
75A VAL* 4.3 15.0 - - + -
76A ARG 2.9 8.7 + - - -
77A LEU* 3.7 26.0 - - + -
78A GLN* 2.8 35.2 + - - +
100A VAL* 3.6 17.7 - - + -
189A VAL* 4.8 4.9 - - + -
192A ILE* 3.5 35.4 - - + -
193A LEU* 4.0 22.4 - - + -
196A HIS* 3.8 26.5 - + - -
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Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU 4.3 1.0 + - - -
26A PHE* 1.3 69.8 - - - +
28A VAL* 1.3 61.1 + - - +
29A LEU* 4.7 1.1 - - + -
78A GLN* 3.7 13.4 - - - +
80A TRP* 3.2 56.3 - - + +
94A VAL 4.3 2.8 + - - -
95A TYR 2.8 25.6 + - - -
97A LYS* 2.5 39.6 + - - +
98A GLU* 4.0 11.9 - - + +
99A ALA* 3.6 18.3 - - + +
100A VAL* 3.0 33.1 + - - +
101A GLY 3.7 1.0 + - - +
551D TYR* 5.5 3.8 + - - -
553D VAL* 5.2 8.5 - - + +
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Residues in contact with VAL 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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26A PHE* 4.0 11.4 - - + +
27A LYS* 1.3 78.8 - - - +
29A LEU* 1.3 74.6 + - - +
77A LEU* 4.1 21.3 - - + -
78A GLN 2.8 14.3 + - - +
79A LEU* 3.5 19.1 - - + +
80A TRP* 2.9 26.9 + - - -
101A GLY 3.2 17.0 - - - +
103A PHE* 4.4 5.4 - - + -
188A LEU* 3.8 18.8 - - + -
192A ILE* 4.2 20.6 - - + -
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Residues in contact with LEU 29 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A LYS* 4.7 1.8 - - - -
28A VAL* 1.3 76.3 - - - +
30A VAL* 1.3 63.5 + - - +
31A ILE* 4.2 10.1 - - + -
80A TRP* 3.8 17.0 - - + -
82A ILE* 3.8 18.4 - - + -
95A TYR 3.7 21.5 - - - +
96A TYR* 3.5 28.0 - - + -
99A ALA* 3.8 25.4 - - + -
101A GLY 3.0 8.3 + - - +
102A ALA* 3.4 8.7 - - + -
103A PHE 2.8 26.7 + - - -
124A LEU* 3.5 23.1 - - + -
136A ILE* 4.9 0.2 - - + -
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Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A VAL 4.6 0.9 - - - +
29A LEU* 1.3 78.6 - - - +
31A ILE* 1.3 64.5 + - - +
38A LYS* 3.7 35.2 - - + +
41A ILE* 5.6 4.7 - - + -
42A ILE* 3.7 31.0 - - + -
79A LEU* 4.4 12.3 - - + -
80A TRP 3.0 12.1 + - - +
81A ASP* 4.1 1.3 - - - -
82A ILE* 3.2 23.6 + - - +
103A PHE* 3.4 22.9 - - + -
105A VAL* 4.1 15.0 - - + -
141A LEU* 6.1 0.2 - - + -
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Residues in contact with ILE 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 LEU* 4.2 7.4 - - + -
30A VAL* 1.3 84.4 - - - +
32A GLY* 1.3 59.4 + - - +
38A LYS* 3.3 12.0 - - - +
82A ILE* 3.9 28.9 - - + -
96A TYR* 4.2 13.2 - - + +
102A ALA* 5.2 2.9 - - + -
103A PHE 2.9 17.2 + - - +
104A VAL* 3.4 22.3 - - + -
105A VAL* 2.9 25.6 + - - +
120A TRP* 3.9 41.3 - - + +
124A LEU* 4.5 19.7 - - + -
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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