Contacts of the helix formed by residues 96 - 105 (chain D) in PDB entry 2YPT
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 GLY 96 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92D ILE 3.0 5.6 + - - -
93D LEU* 3.2 9.6 + - - -
94D LEU 3.2 4.2 - - - -
95D PHE* 1.3 80.6 - - - +
97D GLY* 1.3 64.7 + - - +
99D PRO* 3.5 22.1 - - - +
100D TYR* 3.5 16.3 + - - +
376D PHE 5.4 2.0 - - - -
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Residues in contact with GLY 97 (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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92D ILE* 2.8 28.9 + - - -
95D PHE* 3.6 7.3 - - - +
96D GLY* 1.3 70.6 - - - +
98D ILE* 1.4 53.3 + - - +
99D PRO* 4.0 0.2 - - - +
100D TYR* 3.2 9.5 + - - +
101D LEU* 2.7 38.7 + - - +
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Residues in contact with ILE 98 (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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92D ILE* 4.1 18.8 - - + +
93D LEU* 3.8 31.0 - - + -
97D GLY* 1.4 71.5 - - - +
99D PRO* 1.4 62.2 - - + +
101D LEU* 3.4 8.2 + - - +
102D TRP* 3.0 27.2 + - - +
126D PHE* 3.7 25.6 - - + -
376D PHE* 5.6 4.3 - - + -
378D PHE* 3.9 9.0 - - + -
386D ILE* 3.9 16.4 - - + -
389D LEU* 4.9 6.1 - - + -
394D PHE* 4.8 12.6 - - + -
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Residues in contact with PRO 99 (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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96D GLY* 3.5 22.7 - - - +
98D ILE* 1.4 93.8 - - + +
100D TYR* 1.3 54.2 + - - +
102D TRP* 3.3 5.2 - - - +
103D ARG* 3.1 43.7 + - - +
376D PHE 3.4 26.2 - - - +
377D GLY* 4.0 19.1 - - - +
378D PHE* 3.5 28.9 - - + -
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Residues in contact with TYR 100 (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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95D PHE* 6.3 3.1 - + - -
96D GLY 3.5 16.7 + - - +
97D GLY* 3.2 6.6 + - - +
99D PRO* 1.3 76.4 - - - +
101D LEU* 1.4 65.0 + - - +
103D ARG* 3.3 29.4 + - + +
104D LEU* 3.1 61.4 + - + +
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Residues in contact with LEU 101 (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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97D GLY 2.7 22.0 + - - +
98D ILE* 3.7 6.7 - - + +
100D TYR* 1.4 73.3 - - - +
102D TRP* 1.4 62.6 + - - +
104D LEU* 3.5 15.0 + - + +
105D SER* 3.2 21.7 + - - -
126D PHE* 3.8 23.8 - - + -
129D LEU* 4.3 17.3 - - + -
130D ALA* 4.3 24.9 - - + +
133D PHE* 3.6 32.1 - - + -
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Residues in contact with TRP 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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98D ILE 3.0 13.9 + - - +
99D PRO 3.3 11.7 - - - +
101D LEU* 1.4 73.8 - - - +
103D ARG* 1.3 64.1 + - + +
105D SER* 2.8 19.1 + - - -
119D GLU* 4.2 8.1 - - + -
122D GLN* 3.0 52.7 + - + +
123D SER* 3.2 45.8 - - - -
126D PHE* 3.5 34.9 - + + -
378D PHE* 4.1 19.3 - + + -
381D SER* 4.6 7.5 + - - -
383D PRO* 3.5 33.1 - - + +
385D LEU* 4.2 5.2 - - + -
386D ILE* 3.8 18.2 - - + -
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Residues in contact with ARG 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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99D PRO* 3.1 27.3 + - - +
100D TYR* 3.3 31.3 + - + +
102D TRP* 1.3 80.3 - - + +
104D LEU* 1.4 62.6 + - + +
106D GLY* 3.3 15.8 + - - -
107D ARG* 4.9 1.0 + - - +
122D GLN* 4.8 2.9 - - - +
377D GLY 4.2 16.8 + - - -
379D TYR* 5.6 3.2 - - - -
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Residues in contact with LEU 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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100D TYR* 3.1 60.3 + - + +
101D LEU* 3.5 16.1 + - + +
102D TRP 3.4 0.2 - - - -
103D ARG* 1.4 75.7 - - + +
105D SER* 1.3 56.5 + - - +
106D GLY 3.2 8.2 + - - +
129D LEU* 5.2 5.1 - - + +
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Residues in contact with SER 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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101D LEU 3.2 13.3 + - - -
102D TRP* 2.8 25.2 + - - -
103D ARG 3.2 0.2 - - - -
104D LEU* 1.3 75.7 - - - +
106D GLY* 1.3 61.6 + - - +
122D GLN* 3.4 14.8 + - - +
125D VAL* 3.2 37.6 - - - +
126D PHE* 3.5 24.5 - - - +
129D LEU* 4.0 11.4 - - - -
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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