Contacts of the helix formed by residues 88 - 99 (chain A) in PDB entry 5CTS
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 LEU 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A LEU* 4.8 1.8 - - - +
79A PRO* 3.1 16.1 + - + +
80A LYS 4.0 17.9 - - - +
81A GLY* 3.4 24.9 - - - +
86A GLU 4.3 1.1 - - - +
87A PRO* 1.3 73.2 - - - +
89A PRO* 1.3 69.0 - - - +
90A GLU* 3.9 15.9 - - - +
91A GLY* 3.1 11.1 + - - +
92A LEU* 3.5 7.6 + - - +
107A VAL* 3.8 28.9 - - + -
111A SER* 5.2 1.6 - - - +
208A ASP* 3.9 17.9 - - + +
229A ARG* 3.3 32.5 - - - +
233A THR* 3.8 2.0 + - - -
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Residues in contact with PRO 89 (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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87A PRO 3.6 8.1 - - - +
88A LEU* 1.3 81.0 - - + +
90A GLU* 1.3 69.2 + - - +
92A LEU* 3.1 9.3 + - + +
93A PHE* 2.9 22.7 + - - +
114A TRP* 5.0 0.9 - - - -
209A TRP* 3.9 17.0 - - + -
210A SER* 3.3 27.1 - - - +
229A ARG* 3.8 8.1 - - + +
232A LEU* 3.9 17.9 - - + +
233A THR* 3.5 14.1 - - - +
403A LEU* 3.6 26.1 - - + +
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Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 3.0 9.4 - - + +
89A PRO* 1.3 91.6 - - - +
91A GLY* 1.3 60.6 + - - +
93A PHE* 3.2 6.4 + - - +
94A TRP 3.1 17.0 + - - -
107A VAL* 4.0 17.3 - - + -
110A LEU* 3.2 20.5 - - + +
111A SER* 2.6 39.0 + - - +
114A TRP* 3.9 25.7 - - + -
208A ASP* 3.1 9.5 - - - +
209A TRP* 2.9 38.3 + - - +
210A SER 4.7 0.3 + - - -
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Residues in contact with GLY 91 (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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78A LEU* 4.1 9.6 - - - -
79A PRO* 5.3 3.1 - - - -
88A LEU* 3.1 9.3 + - - -
90A GLU* 1.3 75.5 - - - +
92A LEU* 1.3 60.1 + - - +
94A TRP* 3.3 1.7 + - - -
95A LEU* 2.9 27.4 + - - +
102A PRO* 3.3 28.4 - - - +
107A VAL* 3.8 14.0 - - - +
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Residues in contact with LEU 92 (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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66A PHE* 4.3 23.8 - - + -
74A CYS* 4.6 1.3 - - - -
78A LEU* 3.9 25.3 - - + +
88A LEU 3.5 4.6 + - - +
89A PRO* 3.1 17.2 + - + +
91A GLY* 1.3 77.0 - - - +
93A PHE* 1.3 57.2 + - - +
95A LEU* 3.0 20.0 + - + +
96A LEU* 2.8 35.7 + - + +
233A THR* 3.1 29.4 - - + +
236A SER* 2.7 36.8 - - - +
403A LEU* 5.2 0.4 - - + -
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Residues in contact with PHE 93 (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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6A LEU* 3.7 25.1 - - + -
89A PRO 2.9 11.7 + - - +
90A GLU 3.2 9.8 + - - +
92A LEU* 1.3 76.7 - - - +
94A TRP* 1.3 63.4 + - - +
96A LEU* 3.2 7.5 + - - +
97A VAL* 3.0 46.9 + - + +
110A LEU* 4.0 12.6 - - + -
114A TRP* 3.6 24.9 - + + -
175A ALA* 5.7 1.1 - - + -
176A MET* 3.8 23.8 - - + -
179A ILE* 3.7 22.0 - - + -
403A LEU* 3.8 33.8 - - + +
406A LEU* 5.1 0.9 - - + -
407A ALA* 4.1 7.6 - - + -
410A ILE* 5.0 10.5 - - + -
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Residues in contact with TRP 94 (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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4A THR* 3.7 28.5 - - + -
6A LEU* 4.0 38.4 - - + -
9A VAL* 4.4 18.6 - - + +
90A GLU 3.1 6.7 + - - -
91A GLY 3.6 7.6 - - - +
93A PHE* 1.3 79.4 - - - +
95A LEU* 1.3 63.2 + - - +
97A VAL* 4.6 3.4 - - - -
98A THR* 2.8 66.2 + - + +
100A GLN* 3.6 16.7 + - - +
102A PRO* 3.6 21.4 - - + +
106A GLN* 3.5 38.4 + - + +
109A TRP* 4.1 10.1 - + - -
110A LEU* 3.5 29.6 - - + -
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Residues in contact with LEU 95 (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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66A PHE* 4.0 26.2 - - + -
67A ARG* 4.7 6.6 - - + +
69A PHE* 3.8 34.5 - - + -
74A CYS* 4.3 10.8 - - - -
78A LEU* 4.4 12.6 - - + -
91A GLY 2.9 14.5 + - - +
92A LEU* 3.0 19.3 + - + +
94A TRP* 1.3 77.9 - - - +
96A LEU* 1.3 58.4 + - - +
99A GLY* 2.7 38.8 + - - +
100A GLN 3.2 30.7 + - - +
101A ILE* 3.9 7.2 - - + +
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Residues in contact with LEU 96 (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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55A THR* 3.2 50.4 - - + +
66A PHE* 3.8 32.5 - - + +
92A LEU* 2.8 28.5 + - + +
93A PHE* 3.7 6.3 - - - +
95A LEU* 1.3 76.7 - - - +
97A VAL* 1.3 61.8 + - - +
99A GLY* 4.3 2.1 + - - -
236A SER* 4.3 12.1 - - - +
237A ASP* 4.2 10.8 - - + +
403A LEU* 3.9 7.6 - - + +
404A GLY* 3.7 31.0 - - - +
407A ALA* 3.9 11.0 - - + -
411A TRP* 4.6 0.9 + - - -
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Residues in contact with VAL 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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6A LEU* 3.9 23.1 - - + -
10A LEU* 3.8 30.0 - - + +
93A PHE* 3.0 39.9 + - + +
94A TRP 3.9 3.4 - - - +
96A LEU* 1.3 75.7 - - - +
98A THR* 1.3 62.6 + - + +
407A ALA* 3.6 26.2 - - + +
410A ILE* 4.9 6.5 - - + -
411A TRP* 2.5 39.6 + - + +
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Residues in contact with THR 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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6A LEU* 3.6 31.4 - - + -
9A VAL* 4.1 16.8 - - + -
10A LEU* 5.6 0.4 - - + -
13A LEU* 3.8 30.2 - - + +
94A TRP* 2.8 41.9 + - + +
97A VAL* 1.3 81.6 - - + +
99A GLY* 1.3 56.2 + - - +
100A GLN* 2.9 31.5 + - - +
411A TRP* 5.7 0.2 - - - -
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Residues in contact with GLY 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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67A ARG* 2.8 46.3 + - - -
95A LEU* 2.7 25.9 + - - +
96A LEU 4.3 2.0 + - - -
97A VAL 3.7 1.2 - - - -
98A THR* 1.3 72.6 - - - +
100A GLN* 1.3 59.1 + - - +
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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