Contacts of the strand formed by residues 23 - 31 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C ARG* 1.3 79.2 - - - +
24C HIS* 1.3 68.4 + - - +
74C LEU* 3.2 27.1 - - + +
76C ARG* 2.9 31.4 + - - -
554F GLU* 5.6 1.7 - - - +
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Residues in contact with HIS 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ARG* 3.9 30.4 + - + -
23C GLU* 1.3 79.4 - - - +
25C LEU* 1.3 57.7 + - - +
26C PHE* 3.6 36.8 - + + -
73C THR* 3.6 31.0 - - + +
74C LEU 2.9 10.5 + - - +
75C VAL* 4.4 4.4 - - + +
76C ARG* 2.7 38.9 + - - +
193C LEU* 3.8 20.4 - - + +
196C HIS* 5.5 10.6 + - + +
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Residues in contact with LEU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C HIS* 1.3 74.4 - - - +
26C PHE* 1.3 69.8 + - - +
27C LYS 4.3 0.7 + - - -
64C LEU* 4.9 3.1 - - + -
76C ARG* 3.4 35.4 - - + -
78C GLN* 3.9 26.2 - - + +
100C VAL* 5.8 0.9 - - - +
553F VAL* 3.0 55.6 - - + +
554F GLU* 4.7 14.8 - - + +
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Residues in contact with PHE 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C HIS* 3.6 31.0 - + + -
25C LEU* 1.3 79.3 - - - +
27C LYS* 1.3 61.9 + - - +
28C VAL* 3.5 6.2 + - + +
75C VAL* 3.4 32.5 - - + -
76C ARG 2.9 9.7 + - - -
77C LEU* 3.8 16.6 - - + -
78C GLN* 2.8 32.1 + - - +
100C VAL* 3.7 19.1 - - + -
189C VAL* 4.8 5.4 - - + -
192C ILE* 3.5 34.5 - - + -
193C LEU* 4.0 24.2 - - + -
196C HIS* 4.2 23.1 - + - -
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Residues in contact with LYS 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LEU 4.3 0.8 + - - -
26C PHE* 1.3 71.0 - - - +
28C VAL* 1.3 61.3 + - - +
29C LEU* 4.7 1.3 - - + -
78C GLN* 3.7 14.9 + - - +
80C TRP* 3.1 56.5 - - + +
94C VAL 4.3 2.8 + - - -
95C TYR 2.8 26.4 + - - -
97C LYS* 2.5 40.2 + - - +
98C GLU* 4.0 12.1 - - + +
99C ALA* 3.6 18.2 - - + +
100C VAL* 3.0 33.3 + - - +
101C GLY 3.7 0.9 + - - -
551F TYR* 5.5 3.6 + - - -
553F VAL* 5.0 9.4 - - + +
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Residues in contact with VAL 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C PHE* 4.0 11.2 - - + +
27C LYS* 1.3 78.5 - - - +
29C LEU* 1.3 74.3 + - - +
77C LEU* 4.1 22.7 - - + -
78C GLN 2.8 13.5 + - - +
79C LEU* 3.5 18.5 - - + +
80C TRP* 2.8 27.7 + - - +
100C VAL* 4.8 0.2 - - + -
101C GLY 3.2 17.3 - - - +
102C ALA 4.2 0.2 - - - +
103C PHE* 4.3 5.4 - - + -
188C LEU* 3.8 19.3 - - + -
192C ILE* 4.2 20.9 - - + -
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Residues in contact with LEU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C LYS* 4.7 1.8 - - - -
28C VAL* 1.3 75.6 - - - +
30C VAL* 1.3 64.6 + - - +
31C ILE* 4.2 10.1 - - + -
80C TRP* 3.7 21.5 - - + -
82C ILE* 3.8 14.8 - - + -
95C TYR 3.7 21.8 - - - +
96C TYR* 3.5 26.9 - - + -
99C ALA* 3.8 26.0 - - + -
101C GLY 3.0 7.8 + - - +
102C ALA* 3.4 8.7 - - + -
103C PHE 2.8 26.4 + - - -
124C LEU* 3.5 23.3 - - + -
136C ILE* 4.9 0.2 - - + -
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Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C VAL 4.6 0.7 - - - +
29C LEU* 1.3 78.6 - - - +
31C ILE* 1.3 65.2 + - - +
38C LYS* 3.7 36.0 - - + +
41C ILE* 5.6 5.2 - - + -
42C ILE* 3.7 30.5 - - + -
79C LEU* 4.4 12.6 - - + -
80C TRP 2.9 12.5 + - - +
81C ASP* 4.1 1.3 - - - -
82C ILE 3.2 23.4 + - - -
103C PHE* 3.4 22.4 - - + -
105C VAL* 4.1 14.1 - - + -
141C LEU* 6.1 0.4 - - + -
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Residues in contact with ILE 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LEU* 4.2 7.6 - - + -
30C VAL* 1.3 83.7 - - - +
32C GLY* 1.3 59.3 + - - +
38C LYS* 3.3 12.3 - - - +
82C ILE* 3.9 28.0 - - + -
96C TYR* 4.3 13.9 - - + +
102C ALA* 5.2 2.5 - - + -
103C PHE 2.9 17.0 + - - +
104C VAL* 3.4 23.0 - - + -
105C VAL* 2.9 26.3 + - - +
120C TRP* 3.9 41.3 - - + +
124C LEU* 4.5 19.3 - - + -
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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