Contacts of the strand formed by residues 73 - 82 (chain A) in PDB entry 5T4S
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 LYS 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A SER 4.0 9.5 + - - +
72A TYR* 1.3 82.2 - - - +
74A HIS* 1.3 66.3 + - - +
93A SER 3.9 0.3 - - - -
94A GLN* 2.7 74.6 + - + +
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Residues in contact with HIS 74 (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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72A TYR* 3.4 36.7 - - + +
73A LYS* 1.3 77.3 - - - +
75A ASN* 1.3 86.4 + - - +
76A GLY* 3.9 8.9 - - - -
91A PHE* 5.7 3.4 - + - -
92A LEU 5.7 0.2 - - - -
94A GLN* 5.7 0.3 - - - +
401A NAG 3.9 18.4 + - + +
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Residues in contact with ASN 75 (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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72A TYR* 4.7 0.2 + - - -
73A LYS 3.7 1.2 + - - +
74A HIS* 1.3 85.1 + - - +
76A GLY* 1.3 61.3 + - - +
77A THR* 2.7 33.1 + - - -
92A LEU* 3.7 18.4 + - - +
93A SER* 4.6 1.1 - - - +
94A GLN* 6.0 0.2 - - + -
107A MET* 4.1 24.1 - - - +
401A NAG 1.4 82.8 + - - +
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Residues in contact with GLY 76 (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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74A HIS* 3.9 12.5 + - - -
75A ASN* 1.3 73.6 - - - +
77A THR* 1.3 65.0 + - - +
78A GLU* 3.4 9.9 + - - +
91A PHE* 3.7 21.4 - - - +
92A LEU 2.9 19.5 + - - -
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Residues in contact with THR 77 (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 ASN* 2.7 26.0 + - - -
76A GLY* 1.3 74.8 - - - +
78A GLU* 1.3 74.5 + - - +
91A PHE* 3.1 1.1 - - - -
92A LEU* 2.8 44.9 + - + +
401A NAG 4.0 9.4 + - - +
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Residues in contact with GLU 78 (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 GLY 3.4 12.5 + - - +
77A THR* 1.3 87.6 - - - +
79A LEU* 1.3 61.3 + - - +
89A SER* 5.0 4.7 + - - +
90A GLY* 3.2 18.7 - - - +
91A PHE* 4.2 8.6 - - - +
112A THR* 5.5 0.9 + - - -
113A GLU* 5.6 1.4 - - - +
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Residues in contact with LEU 79 (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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43A ASN* 3.6 27.8 - - + +
77A THR 4.5 1.3 - - - +
78A GLU* 1.3 76.4 - - - +
80A THR* 1.3 61.6 + - - +
81A LEU* 3.9 23.0 - - + +
88A VAL 4.2 0.3 - - - +
89A SER* 3.4 3.6 + - - -
90A GLY* 2.9 35.8 + - - +
91A PHE 3.6 33.2 - - - +
92A LEU* 3.7 22.7 - - + +
109A GLY* 3.9 15.5 - - - +
111A VAL* 6.1 1.8 - - + -
137A ILE* 4.2 16.2 - - + +
138A GLY* 6.0 1.3 - - - +
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Residues in contact with THR 80 (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 LEU* 1.3 73.0 - - - +
81A LEU* 1.3 63.3 - - - +
82A ARG* 4.1 16.3 + - + +
87A THR* 3.6 25.4 - - + -
88A VAL 3.4 5.2 - - - +
89A SER* 3.3 18.3 + - - -
137A ILE* 3.6 24.1 - - - +
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Residues in contact with LEU 81 (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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43A ASN* 3.5 41.3 - - + +
44A VAL 5.1 0.2 - - - +
45A TRP* 3.3 42.4 - - + -
79A LEU* 3.9 19.5 - - + -
80A THR* 1.3 73.4 - - - +
82A ARG* 1.3 62.6 + - - +
83A TYR* 3.7 22.8 - - + +
87A THR* 3.4 4.4 - - - +
88A VAL* 2.8 43.8 + - + +
111A VAL* 5.1 2.5 - - + -
137A ILE* 3.9 20.6 - - + -
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Residues in contact with ARG 82 (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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80A THR* 4.1 13.5 + - + -
81A LEU* 1.3 71.3 - - - +
83A TYR* 1.3 66.4 + - - +
86A GLY 4.2 2.2 - - - -
87A THR* 3.7 26.7 - - + +
137A ILE* 5.7 2.4 - - - +
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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