Contacts of the strand formed by residues 73 - 86 (chain A) in PDB entry 5LTU
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 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A CYS* 4.4 13.2 - - - -
35A LEU* 3.9 19.3 - - + -
64A VAL 5.1 0.2 - - - +
67A VAL* 3.3 31.5 + - + +
68A TYR* 3.6 24.8 + - - +
71A ALA* 3.5 15.5 - - + +
72A GLY* 1.3 83.2 - - - +
74A LYS* 1.3 62.1 + - - +
98A LEU* 4.9 3.4 - - + -
100A VAL* 4.2 23.1 - - + -
102A GLU 3.4 10.3 - - - +
103A ILE* 4.5 8.3 - - + -
104A LEU* 5.2 1.1 - - - -
117A ARG* 4.5 4.7 - - - +
119A TRP* 6.4 0.2 - - + -
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Residues in contact with LYS 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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67A VAL* 5.6 1.6 - - - -
68A TYR* 5.5 6.3 - - + -
73A VAL* 1.3 75.5 - - - +
75A GLY* 1.3 58.5 + - - +
98A LEU* 4.8 2.2 - - - -
100A VAL* 3.9 4.1 - - - +
101A THR* 2.9 25.9 + - - +
102A GLU* 3.0 25.5 + - + +
104A LEU* 5.7 4.0 - - + +
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Residues in contact with GLY 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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64A VAL* 5.7 4.0 - - - +
74A LYS* 1.3 77.0 - - - +
76A LYS* 1.3 62.9 + - - -
77A LEU 3.7 2.3 + - - -
98A LEU* 4.0 18.7 - - - +
99A THR 3.1 13.7 - - - -
101A THR* 3.4 12.6 - - - -
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Residues in contact with LYS 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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75A GLY* 1.3 71.2 - - - -
77A LEU* 1.3 73.3 + - - +
78A GLY* 3.4 1.0 + - - -
98A LEU* 4.0 1.6 - - - -
99A THR* 2.9 41.1 + - - +
101A THR* 4.6 6.8 - - + +
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Residues in contact with LEU 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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23A CYS* 4.7 2.5 - - - -
60A GLY* 3.9 31.2 - - - +
63A ALA* 4.5 7.6 - - + -
64A VAL* 4.3 21.8 - - + -
75A GLY 3.7 4.0 + - - -
76A LYS* 1.3 82.7 - - - +
78A GLY* 1.3 67.5 + - - +
96A TYR* 3.7 37.0 - - + -
97A VAL 4.0 4.3 - - - +
98A LEU* 4.2 11.4 - - + +
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Residues in contact with GLY 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 LYS 3.4 3.5 + - - -
77A LEU* 1.3 85.6 - - - +
79A ARG* 1.3 64.9 + - - -
96A TYR* 3.9 5.7 - - - -
97A VAL* 2.8 23.5 + - - -
98A LEU* 5.2 0.4 - - - -
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Residues in contact with ARG 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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31A GLU* 2.9 39.6 + - - -
78A GLY* 1.3 73.4 - - - -
80A LEU* 1.3 70.2 + - - +
81A LEU* 3.4 11.6 + - - +
96A TYR* 3.5 2.9 - - - -
97A VAL* 3.1 47.3 + - + +
143A LEU* 3.4 22.6 + - - +
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Residues in contact with LEU 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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78A GLY 3.9 0.2 + - - -
79A ARG* 1.3 76.4 - - - +
81A LEU* 1.3 62.5 + - - +
82A GLY* 3.6 23.3 - - - +
83A ILE* 4.8 9.0 - - + -
94A TYR* 4.0 22.0 - - + -
95A VAL 3.6 22.9 - - - +
96A TYR* 3.7 38.8 - - + +
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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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24A LEU* 4.2 12.6 - - + -
79A ARG* 3.4 17.0 + - - +
80A LEU* 1.3 73.8 - - - +
82A GLY* 1.3 54.9 + - - +
84A PHE* 4.4 16.6 - - + -
95A VAL* 2.8 25.5 + - + +
97A VAL* 4.9 9.2 - - + -
139A TYR 3.3 27.1 - - - +
142A LYS* 4.6 6.3 - - + +
143A LEU* 4.0 37.5 - - + +
146A GLY* 6.6 0.2 - - - -
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Residues in contact with GLY 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 LEU* 3.4 14.0 - - - +
81A LEU* 1.3 82.4 - - - +
83A ILE* 1.3 65.1 + - - -
84A PHE* 3.7 12.4 - - - -
93A THR 3.5 1.2 - - - +
95A VAL 3.0 24.3 + - - -
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Residues in contact with ILE 83 (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 LEU* 4.8 7.4 - - + -
82A GLY* 1.3 73.3 - - - -
84A PHE* 1.3 63.7 + - - +
85A GLU* 3.7 2.1 + - + +
92A ARG* 4.1 31.9 - - + -
93A THR 3.4 9.4 - - - +
94A TYR* 3.6 42.8 - - + +
203A EDO 3.4 24.3 + - - -
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Residues in contact with PHE 84 (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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81A LEU* 4.4 8.7 - - + -
82A GLY* 3.7 22.4 - - - -
83A ILE* 1.3 73.6 - - - +
85A GLU* 1.3 62.8 + - - +
86A ASN* 3.7 2.6 + - - +
91A HIS 3.9 0.3 - - - +
92A ARG* 3.5 2.4 - - - -
93A THR* 2.8 42.0 + - - +
95A VAL* 3.6 30.3 - - + -
135A VAL 5.6 0.2 - - - -
138A GLU* 4.0 28.5 - - + -
139A TYR* 3.8 39.7 - + + -
142A LYS* 4.1 19.7 - - + -
202A EDO 5.5 3.8 - - - -
203A EDO 4.1 13.0 - - - -
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Residues in contact with GLU 85 (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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17A PHE* 3.5 34.3 - - + -
83A ILE* 3.7 3.4 + - + +
84A PHE* 1.3 70.5 - - - +
86A ASN* 1.3 59.8 + - - +
87A GLN* 2.8 37.2 + - + +
91A HIS 3.5 4.5 - - - +
92A ARG* 2.8 37.8 + - + -
202A EDO 3.3 29.1 + - - +
203A EDO 3.5 15.8 + - - +
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Residues in contact with ASN 86 (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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17A PHE* 4.5 0.2 - - - -
84A PHE 3.7 2.5 + - - +
85A GLU* 1.3 72.3 - - - +
87A GLN* 1.3 59.2 + - - +
88A ASP* 3.0 24.2 + - - +
89A ARG* 3.2 33.3 + - - +
90A LYS* 2.8 23.2 + - - -
91A HIS* 2.8 37.8 + - + +
93A THR* 6.0 0.4 - - - +
135A VAL* 4.2 27.5 - - + +
202A EDO 4.8 7.0 - - - -
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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