Contacts of the helix formed by residues 96 - 105 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A ILE 3.0 6.0 + - - -
93A LEU* 3.7 8.3 - - - -
94A LEU 3.2 4.8 - - - -
95A PHE* 1.3 79.8 - - - +
97A GLY* 1.3 64.3 + - - +
99A PRO* 3.5 21.6 - - - +
100A TYR* 3.6 15.9 + - - +
376A PHE 5.4 2.0 - - - -
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Residues in contact with GLY 97 (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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92A ILE* 2.8 27.4 + - - -
95A PHE* 3.6 3.0 - - - +
96A GLY* 1.3 70.0 - - - +
98A ILE* 1.4 52.6 + - - +
99A PRO* 4.0 0.2 - - - +
100A TYR* 3.2 6.9 + - - +
101A LEU* 2.8 37.2 + - - +
132B LEU* 4.8 7.4 - - - +
136B LEU* 4.7 17.7 - - - -
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Residues in contact with ILE 98 (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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92A ILE* 4.1 19.2 - - + +
93A LEU* 3.8 30.5 - - + -
97A GLY* 1.4 72.8 - - - +
99A PRO* 1.4 68.1 - - + +
101A LEU* 3.4 5.9 + - - -
102A TRP* 3.0 19.8 + - - +
126A PHE* 3.5 27.9 - - + -
376A PHE* 5.6 4.0 - - + -
378A PHE* 3.9 18.6 - - + -
386A ILE* 3.9 6.7 - - + -
389A LEU* 5.2 5.6 - - + -
394A PHE* 4.8 12.8 - - + -
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Residues in contact with PRO 99 (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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96A GLY* 3.5 23.3 - - - +
98A ILE* 1.4 94.3 - - + +
100A TYR* 1.3 54.8 + - - +
102A TRP* 3.3 5.2 + - - +
103A ARG* 3.1 43.5 + - - +
376A PHE 3.4 25.8 - - - +
377A GLY* 4.0 18.8 - - - +
378A PHE* 3.5 28.0 - - + -
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Residues in contact with TYR 100 (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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95A PHE* 6.3 0.7 - + - -
96A GLY 3.6 16.7 + - - +
97A GLY 3.2 2.3 + - - +
99A PRO* 1.3 76.6 - - - +
101A LEU* 1.3 64.4 + - - +
103A ARG* 3.3 29.8 + - + +
104A LEU* 3.1 46.5 + - + +
128B LEU* 3.3 32.5 + - + +
132B LEU* 3.5 43.3 - - + -
171B PHE* 4.0 18.4 - + - -
175B GLN* 3.7 10.6 + - - +
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Residues in contact with LEU 101 (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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97A GLY 2.8 22.3 + - - +
98A ILE* 3.8 6.3 - - - +
100A TYR* 1.3 71.6 - - - +
102A TRP* 1.4 52.3 + - - +
104A LEU* 3.1 7.2 + - - +
105A SER* 2.8 34.9 + - - +
126A PHE* 3.7 23.8 - - + +
129A LEU* 4.1 10.1 - - + -
130A ALA* 4.2 29.8 - - + +
133A PHE* 3.7 30.3 - - + -
129B LEU* 3.8 20.6 - - + -
132B LEU* 4.2 13.7 - - + -
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Residues in contact with TRP 102 (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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98A ILE 3.0 14.4 + - - +
99A PRO 3.3 11.2 - - - +
100A TYR 3.2 0.2 - - - -
101A LEU* 1.4 76.5 - - - +
103A ARG* 1.3 59.8 + - + +
105A SER* 3.2 13.4 + - - -
119A GLU* 4.1 9.0 - - + -
122A GLN* 2.8 60.1 + - + +
123A SER* 3.3 45.3 - - - -
126A PHE* 3.5 36.5 - + + -
378A PHE* 4.0 19.5 - + + -
381A SER* 4.6 7.3 + - - -
383A PRO* 3.5 34.0 - - + +
385A LEU* 4.2 5.6 - - + -
386A ILE* 3.7 19.5 - - + -
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Residues in contact with ARG 103 (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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99A PRO* 3.1 27.1 + - - +
100A TYR* 3.5 29.5 - - + +
101A LEU 3.3 0.4 - - - -
102A TRP* 1.3 78.6 - - + +
104A LEU* 1.4 61.9 + - + +
106A GLY* 3.3 15.4 + - - -
107A ARG 4.9 0.2 + - - -
122A GLN* 4.7 2.5 - - - +
377A GLY 4.2 16.8 + - - -
379A TYR* 5.6 3.2 - - - -
380A ASP* 4.8 11.7 + - - -
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Residues in contact with LEU 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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100A TYR* 3.1 51.0 + - + +
101A LEU* 3.1 8.7 + - - +
103A ARG* 1.4 72.2 - - + +
105A SER* 1.3 56.6 + - - +
106A GLY 3.2 10.3 + - - +
129A LEU* 5.2 0.7 - - - +
125B VAL* 3.8 26.7 - - + +
128B LEU* 3.6 43.7 - - + +
129B LEU* 3.8 31.9 - - + +
132B LEU* 3.9 10.8 - - + -
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Residues in contact with SER 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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101A LEU 2.8 15.7 + - - -
102A TRP* 3.2 15.0 + - - -
103A ARG 3.3 0.6 - - - -
104A LEU* 1.3 74.7 - - - +
106A GLY* 1.3 58.4 + - - +
122A GLN* 3.2 18.8 + - - +
125A VAL* 3.3 34.2 - - - +
126A PHE* 3.4 31.7 - - - +
129A LEU* 4.1 13.5 - - - -
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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