Contacts of the helix formed by residues 103 - 107 (chain A) in PDB entry 4KEU
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 PRO 103 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A MET* 3.9 27.1 - - + -
98A ILE* 4.5 3.6 - - + -
101A ASP 4.4 2.0 - - - +
102A LEU* 1.3 96.8 - - + +
104A PHE* 1.3 68.6 + - + +
105A TYR 2.9 3.4 + - - -
106A PHE* 3.0 31.5 + - + +
107A LEU* 4.3 1.4 + - - +
29C SER* 3.8 23.6 - - - +
31C ALA* 5.0 5.4 - - + -
32C VAL* 4.0 11.2 - - + -
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Residues in contact with PHE 104 (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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102A LEU 3.6 3.1 + - - -
103A PRO* 1.3 73.1 - - + +
105A TYR* 1.3 62.1 - - - +
106A PHE 3.0 1.6 + - - -
107A LEU* 3.1 39.1 + - + +
29C SER* 4.0 6.0 + - - +
71C GLY* 4.5 14.8 - - - -
72C LEU* 5.4 3.6 - - + -
97C TYR* 3.8 35.0 - + - -
98C ILE* 5.2 0.7 - - - -
99C TYR* 3.2 54.5 - + + -
262C ASP* 5.8 1.1 - - - +
263C MET* 3.3 27.3 - - + +
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Residues in contact with TYR 105 (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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103A PRO 2.9 1.1 + - - +
104A PHE* 1.3 77.9 - - - +
106A PHE* 1.3 88.8 + + - +
109A ARG* 2.8 63.1 + - - -
113A GLU* 4.8 1.2 + - - -
117A LEU* 4.9 3.6 - - + +
29C SER* 3.4 19.4 + - - +
32C VAL* 3.9 16.6 - - + -
39C LEU* 3.3 40.5 - - + +
40C TYR* 3.9 8.7 - + - -
262C ASP* 3.0 52.6 + - + +
263C MET* 3.9 7.6 - - - +
264C GLY 3.5 8.5 + - - -
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Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A MET* 4.6 1.6 - - - -
96A ILE* 3.8 16.4 - - + -
102A LEU* 3.7 36.1 - - + +
103A PRO* 3.0 29.8 + - + +
105A TYR* 1.3 94.5 - + - +
107A LEU* 1.3 66.2 + - - +
108A ASN 3.1 0.9 + - - -
109A ARG* 3.0 30.6 + - + +
113A GLU 5.9 0.7 - - - -
114A ILE* 3.7 28.5 - - + -
117A LEU* 3.5 32.1 - - + -
151A LYS* 5.7 4.4 - - + +
32C VAL* 3.7 25.4 - - + -
36C TRP* 4.5 4.3 - + - -
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Residues in contact with LEU 107 (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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103A PRO 4.3 1.0 + - - +
104A PHE* 3.1 38.2 + - + +
106A PHE* 1.3 76.3 - - - +
108A ASN* 1.3 70.2 + - - +
109A ARG* 4.1 0.2 - - - +
99C TYR* 6.1 1.3 - - + -
263C MET* 3.6 25.1 - - + -
264C GLY 3.4 7.1 + - - -
265C THR* 3.3 27.8 + - - +
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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