Contacts of the strand formed by residues 91 - 98 (chain A) in PDB entry 5TSW
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 VAL 91 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A SER* 3.2 4.7 - - - -
82A ARG* 2.9 57.0 + - + +
84A ALA* 5.9 0.9 - - + +
89A THR* 4.0 7.9 - - + +
90A LYS* 1.3 76.0 - - - +
92A ASN* 1.3 75.6 + - - +
93A LEU 3.4 0.2 + - - -
33B ALA* 5.8 3.4 - - + -
34B ASN* 3.8 23.1 - - - +
147B SER* 5.8 3.1 - - - -
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Residues in contact with ASN 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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79A THR* 3.1 20.8 + - - +
80A ILE 4.2 2.0 - - - -
81A SER* 3.9 7.2 + - - +
91A VAL* 1.3 85.1 - - - +
93A LEU* 1.3 62.3 + - - +
95A SER* 3.2 23.6 + - - -
34B ASN* 4.9 2.3 + - - +
146B GLU* 5.1 5.9 - - - +
147B SER* 2.8 49.1 + - - +
148B GLY 4.6 0.2 + - - -
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Residues in contact with LEU 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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58A ILE* 3.5 25.6 - - + -
80A ILE 3.0 14.3 + - - +
81A SER 4.4 1.3 - - - -
82A ARG* 3.6 32.5 - - + +
91A VAL 3.4 0.6 + - - +
92A ASN* 1.3 76.0 - - - +
94A LEU* 1.3 75.2 + - + +
124A PHE* 3.5 41.2 - - + -
126A LEU* 4.5 3.8 - - + -
132A LEU* 3.7 13.7 - - + -
15B HIS* 4.9 2.6 + - - -
34B ASN* 3.5 32.1 - - + +
148B GLY* 3.4 13.6 - - - -
151B TYR* 4.9 0.7 - - - -
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Residues in contact with LEU 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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58A ILE* 4.0 6.3 - - + +
79A THR* 3.3 5.4 + - - -
80A ILE* 3.2 41.8 + - + +
93A LEU* 1.3 92.2 + - + +
95A SER* 1.3 66.7 + - - +
120A LEU* 3.7 19.1 - - + -
121A GLY* 3.2 39.7 - - - +
122A GLY 3.8 2.7 - - - +
124A PHE* 3.4 21.8 - - + -
15B HIS* 4.5 2.5 - - + -
148B GLY* 3.6 4.9 - - - +
151B TYR* 3.6 31.4 - - + -
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Residues in contact with SER 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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77A THR* 5.9 0.2 - - - -
78A HIS 3.5 6.5 + - - -
79A THR* 3.4 17.0 - - - +
92A ASN* 3.2 25.2 + - - -
94A LEU* 1.3 78.4 - - - +
96A ALA* 1.3 65.4 + - - +
97A ILE* 5.0 2.9 - - - +
120A LEU* 4.3 4.1 - - - +
61B GLN* 3.0 20.0 + - - +
63B LEU* 4.8 0.3 - - - +
147B SER 3.7 7.4 - - - -
148B GLY 2.9 11.6 + - - +
149B GLN* 3.5 22.7 + - - +
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Residues in contact with ALA 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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76A LEU 4.5 0.2 - - - -
77A THR* 3.5 3.6 - - - -
78A HIS 3.0 29.6 + - - +
95A SER* 1.3 77.5 + - - +
97A ILE* 1.3 70.7 + - - +
118A ILE* 3.4 32.3 - - + +
120A LEU* 3.6 9.6 - - + +
61B GLN* 4.4 5.2 - - - +
63B LEU* 4.8 5.6 - - - -
117B PRO* 4.2 17.0 - - + -
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Residues in contact with ILE 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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75A LEU* 3.8 27.8 - - + -
76A LEU 3.2 10.3 - - - +
77A THR* 4.1 18.4 - - + -
95A SER* 5.0 3.1 - - - +
96A ALA* 1.3 83.1 - - - +
98A LYS* 1.3 64.2 + - - +
118A ILE* 4.6 0.7 - - - -
63B LEU* 3.5 16.9 - - + +
115B TYR* 3.4 34.6 - - + +
117B PRO* 3.4 20.9 - - - +
143B ASP* 4.8 1.6 - - - +
149B GLN* 3.4 25.1 - - - +
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Residues in contact with LYS 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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75A LEU* 3.4 9.3 - - - +
76A LEU* 2.8 41.6 + - + +
97A ILE* 1.3 74.4 - - - +
99A SER* 1.3 64.9 + - - +
100A PRO* 3.6 1.5 - - - +
116A GLU* 3.1 36.9 + - + +
117A PRO* 2.6 37.9 + - - +
118A ILE* 3.8 20.9 - - + -
98B LYS* 4.0 23.3 - - - +
115B TYR* 4.1 7.6 - - - +
116B GLU* 4.5 4.5 - - - +
117B PRO* 4.1 15.4 + - + +
98C LYS* 4.0 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