Contacts of the strand formed by residues 87 - 97 (chain D) in PDB entry 5T0I
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 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D GLN* 3.3 27.6 - - - +
84D SER 3.1 25.8 - - - +
85D ILE* 4.2 10.1 - - + -
86D PRO* 1.3 81.5 - - + +
88D VAL* 1.3 62.1 + - - +
89D ILE* 5.7 1.1 - - - +
131D ALA* 3.7 29.4 - - + +
132D LEU 3.1 8.5 - - - +
133D HIS* 4.3 1.1 - - - +
134D LYS* 4.5 3.6 - - - +
140D VAL* 5.2 6.7 - - + -
141D ASP* 6.6 0.2 - - + -
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Residues in contact with VAL 88 (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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87D LEU* 1.3 71.4 - - - +
89D ILE* 1.3 74.7 + - - +
105D SER* 6.6 0.2 - - - -
106D THR* 4.7 7.2 - - - +
131D ALA* 4.4 1.8 - - - -
132D LEU* 2.3 71.5 + - + +
133D HIS 3.3 19.7 - - - +
134D LYS* 4.3 11.9 - - + +
137D ASN* 4.2 6.7 - - - +
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Residues in contact with ILE 89 (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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87D LEU 5.7 0.9 - - - +
88D VAL* 1.3 87.3 - - - +
90D GLY* 1.3 61.5 + - - +
105D SER* 4.7 1.0 - - - -
106D THR* 2.3 40.0 + - + +
129D SER* 3.3 23.6 - - - +
130D VAL 4.0 4.0 - - - +
131D ALA* 4.4 7.9 - - + +
132D LEU* 4.9 1.3 - - - +
143D LEU* 5.8 7.0 - - + -
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Residues in contact with GLY 90 (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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88D VAL 3.7 0.2 + - - -
89D ILE* 1.3 80.0 - - - +
91D GLN* 1.3 58.3 + - - -
103D VAL* 3.8 9.0 - - - -
104D GLY 3.3 9.0 - - - -
106D THR* 4.1 5.4 - - - -
129D SER* 3.2 5.7 + - - -
130D VAL 2.6 45.2 + - - -
132D LEU* 4.2 7.4 - - - -
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Residues in contact with GLN 91 (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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90D GLY* 1.3 66.9 - - - -
92D PHE* 1.3 70.2 + - - +
93D LEU* 4.8 6.1 - - + +
103D VAL* 3.1 2.4 - - - -
104D GLY* 2.3 63.2 + - - +
105D SER 4.7 4.8 - - - +
106D THR* 5.6 0.6 - - - +
127D ASN* 5.3 8.7 + - + +
128D ALA 3.6 9.2 - - - +
129D SER* 4.4 3.1 - - - +
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Residues in contact with PHE 92 (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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90D GLY 4.0 1.2 + - - -
91D GLN* 1.3 85.6 + - - +
93D LEU* 1.3 57.6 + - - +
94D GLU* 3.4 36.6 - - - -
95D ALA 3.7 0.9 - - - -
101D ALA* 3.5 25.8 - - + -
102D ILE 3.7 9.0 - - - -
103D VAL* 4.0 8.2 - - + +
115D ILE* 5.7 0.4 - - + -
124D LEU* 3.6 33.9 - - + +
125D LYS 3.1 27.8 - - - -
126D PRO* 3.2 13.0 - - + -
127D ASN* 3.5 19.2 - - - +
128D ALA* 2.6 26.6 + - + +
130D VAL* 4.1 17.2 - - + +
139D LEU* 4.6 8.5 - - + -
142D VAL* 5.9 0.4 - - + -
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Residues in contact with LEU 93 (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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113C ARG* 3.8 24.2 - - - +
130C LYS* 5.6 4.5 - - - +
91D GLN* 3.7 6.2 + - + +
92D PHE* 1.3 75.3 - - - +
94D GLU* 1.3 66.3 + - + +
102D ILE* 3.4 36.2 + - + +
104D GLY* 4.8 7.2 - - - +
110D ASN* 3.5 29.6 - - - +
126D PRO* 2.7 20.9 - - - +
127D ASN* 3.1 12.3 - - - +
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Residues in contact with GLU 94 (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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113C ARG* 2.9 31.6 + - - -
127C LEU* 4.5 0.5 - - - +
128C PRO* 3.2 21.6 - - - +
130C LYS* 4.4 11.1 + - - +
92D PHE* 3.4 18.6 - - - -
93D LEU* 1.3 85.0 - - + +
95D ALA* 1.3 64.2 + - - +
96D VAL* 4.1 13.9 - - + +
102D ILE* 3.3 40.6 + - + +
126D PRO* 4.2 2.9 - - - -
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Residues in contact with ALA 95 (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 PHE* 3.7 5.1 - - - -
94D GLU* 1.3 75.5 - - - +
96D VAL* 1.3 64.9 + - - +
97D ASP 3.6 6.3 - - - +
101D ALA* 4.3 5.6 - - + -
124D LEU* 3.7 37.9 - - + +
126D PRO* 6.0 0.4 - - - +
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Residues in contact with VAL 96 (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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125C LYS* 6.1 0.2 - - + -
126C ILE 5.5 0.7 - - - +
127C LEU* 3.5 41.7 - - + -
128C PRO* 4.8 9.6 - - + +
94D GLU* 3.6 10.9 + - + +
95D ALA* 1.3 76.4 - - - +
97D ASP* 1.3 87.5 + - - +
100D THR 3.9 9.6 + - - +
101D ALA* 4.1 9.9 - - - -
102D ILE* 4.0 25.8 - - + -
112D TYR* 4.3 12.8 - - + -
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Residues in contact with ASP 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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125C LYS* 3.2 31.6 + - - +
95D ALA* 3.6 5.5 - - - +
96D VAL* 1.3 94.5 + - - +
98D GLN* 1.3 67.3 + - - +
99D ASN 3.8 0.3 + - - -
100D THR* 2.8 32.1 - - - +
112D TYR* 4.9 0.2 - - - -
115D ILE* 5.4 1.7 - - - +
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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