Contacts of the strand formed by residues 25 - 30 (chain C) in PDB entry 4IXU
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 SER 25 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24C HIS* 1.3 77.6 + - - +
26C VAL* 1.3 60.6 + - - +
64C HIS* 3.4 14.5 - - - +
110C GLY 4.2 13.3 + - - +
111C TYR* 3.5 25.7 - - - -
112C SER* 2.9 29.3 + - - -
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Residues in contact with VAL 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* 4.8 3.4 - - + +
25C SER* 1.3 80.1 - - - +
27C ALA* 1.3 66.2 + - - +
28C VAL* 4.1 9.4 + - + -
58C LEU* 4.4 6.7 - - + -
63C CYS* 3.8 25.4 - - + -
64C HIS 2.9 6.8 + - - +
65C LEU* 3.4 19.1 - - + +
66C LYS 3.0 22.2 + - - -
111C TYR* 3.6 3.3 - - - -
112C SER* 3.3 6.7 - - - +
114C VAL* 3.7 29.6 - - + -
323C PHE* 3.6 27.1 - - + -
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Residues in contact with ALA 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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26C VAL* 1.3 74.0 - - - +
28C VAL* 1.3 60.5 + - - +
29C ILE* 4.1 1.1 - - + -
66C LYS 3.3 4.9 - - - +
68C PHE* 3.6 27.1 - - + -
106C ALA* 4.0 10.3 - - + -
111C TYR* 3.7 25.3 - - + -
112C SER 2.8 8.7 + - - +
113C CYS* 4.6 6.0 - - - -
114C VAL* 2.8 33.1 + - - +
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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
----------------------------------------------------------
26C VAL* 4.2 14.1 - - + -
27C ALA* 1.3 76.9 - - - +
29C ILE* 1.3 63.5 + - - +
50C ARG* 4.2 11.9 - - - +
54C LEU* 4.2 5.2 - - + -
55C MET* 3.8 40.4 - - + -
58C LEU* 4.2 13.5 - - + -
65C LEU* 4.6 3.4 - - + -
66C LYS 2.8 11.0 + - - +
67C ASP* 3.5 4.8 - - - +
68C PHE* 2.8 30.5 + - - +
69C GLY 4.1 0.2 + - - -
114C VAL* 3.4 8.5 - - + +
116C LEU* 4.0 28.7 - - + -
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Residues in contact with ILE 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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28C VAL* 1.3 81.4 - - - +
30C GLY* 1.3 67.3 + - - +
31C ALA 3.6 0.3 + - - -
50C ARG* 4.5 0.9 - - - -
68C PHE* 3.9 18.4 - - + -
69C GLY 4.0 2.0 - - - -
71C LEU* 3.7 34.5 - - + -
99C LEU* 4.1 10.5 - - + -
102C VAL* 3.7 21.8 - - + +
103C VAL* 4.1 15.5 - - + +
106C ALA* 4.9 2.2 - - + -
113C CYS* 3.5 30.1 - - - -
114C VAL 2.8 13.9 + - - +
115C THR* 3.3 7.3 - - + +
116C LEU* 2.8 27.6 + - - -
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Residues in contact with GLY 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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29C ILE* 1.3 72.0 - - - +
31C ALA* 1.3 59.2 + - - -
32C PRO* 3.4 6.5 - - - -
46C PRO* 4.0 8.7 - - - -
50C ARG* 3.8 5.0 - - - +
69C GLY 2.9 11.7 + - - -
70C ASP* 3.4 22.0 - - - -
71C LEU* 2.9 33.3 + - - +
116C LEU* 3.8 6.1 - - - -
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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