Contacts of the helix formed by residues 100 - 105 (chain D) in PDB entry 3P05
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 ARG 100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80D TRP* 4.1 2.0 - - - -
81D ASP* 3.7 14.4 - - - +
84D HIS 6.0 0.9 - - - -
97D ARG* 5.5 0.2 - - - +
98D GLU 3.7 2.6 + - - +
99D PRO* 1.3 75.2 - - - +
101D GLY* 1.3 69.2 - - - +
102D SER* 3.2 10.1 - - - +
103D ASP* 2.6 29.6 + - - +
104D ILE* 3.2 11.3 + - - +
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Residues in contact with GLY 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D ALA* 3.8 31.4 - - - +
80D TRP* 3.7 8.6 - - - -
81D ASP* 2.8 23.7 + - - -
100D ARG* 1.3 70.3 - - - +
102D SER* 1.3 59.9 + - - +
104D ILE* 3.2 7.8 + - - +
105D ALA* 3.1 17.5 + - - +
133D TRP* 3.6 10.2 - - - -
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Residues in contact with SER 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D ALA* 4.4 4.0 - - - +
81D ASP* 5.1 1.0 + - - -
100D ARG* 4.4 8.3 - - - +
101D GLY* 1.3 72.2 - - - +
103D ASP* 1.3 61.8 + - - +
104D ILE 3.3 0.2 - - - -
105D ALA* 3.5 6.2 + - - +
106D GLY 3.2 2.6 + - - -
107D THR* 3.1 44.6 + - - -
108D THR* 2.8 31.2 + - - +
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Residues in contact with ASP 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D PRO* 4.6 4.2 - - - +
97D ARG* 2.9 43.7 + - - -
99D PRO* 3.5 4.4 - - + -
100D ARG* 2.6 40.1 + - - +
102D SER* 1.3 76.6 + - - +
104D ILE* 1.3 59.3 + - - +
106D GLY* 3.1 9.4 + - - -
108D THR* 2.9 24.7 + - - +
109D SER* 2.9 23.3 + - - -
114D GLN* 4.7 0.2 - - - +
117D TRP* 3.8 21.6 - - + -
126D VAL* 5.3 0.3 - - - +
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Residues in contact with ILE 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D PRO* 3.4 8.1 - - - +
80D TRP* 3.4 50.3 - - + +
99D PRO* 4.3 6.1 - - + +
100D ARG 3.7 7.2 - - - +
101D GLY 3.2 7.3 + - - +
103D ASP* 1.3 73.7 - - - +
105D ALA* 1.3 55.1 + - - +
106D GLY 3.0 8.3 + - - -
126D VAL* 3.8 32.8 - - + +
129D ILE* 3.9 11.7 - - + -
130D TYR* 3.3 41.0 - - + +
133D TRP* 3.6 25.6 - - + -
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Residues in contact with ALA 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D ASN* 3.0 19.2 + - - -
73D ILE* 4.0 16.2 - - + -
77D ALA* 5.6 1.3 - - + -
101D GLY 3.1 13.8 + - - +
102D SER* 3.5 8.5 + - - +
103D ASP 3.3 0.4 - - - -
104D ILE* 1.3 75.2 - - - +
106D GLY* 1.3 59.3 + - - +
107D THR* 3.2 13.9 + - + +
130D TYR* 3.4 37.4 + - + +
133D TRP* 4.7 3.1 - - + -
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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