Contacts of the strand formed by residues 91 - 103 (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 HIS 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A PHE* 3.6 4.0 - - - -
18A LYS* 3.4 39.0 + - + +
20A ARG* 3.7 26.9 - - - +
85A GLU* 3.5 0.7 - - - -
86A ASN* 2.8 44.9 + - + +
89A ARG* 3.3 57.7 + - + +
90A LYS* 1.3 78.4 + - - +
92A ARG* 1.3 68.2 + - - +
93A THR* 4.2 12.1 - - - +
201A EDO 4.9 6.1 + - - -
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Residues in contact with ARG 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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13A ASP* 3.0 33.3 + - - +
15A GLU* 3.0 33.1 + - - -
17A PHE* 3.7 27.6 - - + -
18A LYS 2.9 14.3 + - - +
19A LYS* 3.7 5.6 - - + -
20A ARG 3.0 23.7 + - - +
83A ILE* 4.1 17.7 - - + -
84A PHE 3.5 4.3 - - - -
85A GLU* 2.8 36.2 + - + +
91A HIS* 1.3 78.1 - - - +
93A THR* 1.3 61.1 + - - +
94A TYR* 4.0 8.1 + - + -
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Residues in contact with THR 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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20A ARG* 3.2 45.2 + - - +
21A ALA* 4.0 2.5 - - - -
22A ALA* 3.9 26.9 - - + +
83A ILE* 3.4 3.4 - - - +
84A PHE* 2.8 46.3 + - - +
86A ASN* 6.0 0.2 - - - +
91A HIS* 4.2 6.4 - - - +
92A ARG* 1.3 73.9 - - - +
94A TYR* 1.3 65.9 + - - +
95A VAL* 3.4 6.8 + - + +
139A TYR* 3.9 16.2 + - - +
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Residues in contact with TYR 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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19A LYS* 4.5 18.3 + - + -
20A ARG 3.0 21.3 + - - +
21A ALA* 3.3 6.1 - - + +
22A ALA 3.0 24.8 + - - +
53A MET* 4.1 17.9 - - - -
59A PRO* 3.7 29.1 - - + +
80A LEU* 4.0 17.0 - - + -
82A GLY 3.8 4.5 - - - -
83A ILE* 3.6 39.7 - - + +
92A ARG* 4.4 9.9 - - + -
93A THR* 1.3 70.8 - - - +
95A VAL* 1.3 61.5 + - - +
96A TYR* 3.9 18.6 + - + -
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Residues in contact with VAL 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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22A ALA* 3.4 9.6 - - + +
23A CYS 5.2 0.2 - - - -
24A LEU* 4.2 21.8 - - + -
80A LEU* 3.6 2.2 - - - +
81A LEU* 2.8 41.5 + - + +
82A GLY 3.0 9.4 + - - +
84A PHE* 3.6 31.4 - - + -
93A THR* 3.9 9.9 - - + +
94A TYR* 1.3 74.2 - - - +
96A TYR* 1.3 64.3 + - - +
139A TYR* 3.8 38.8 - - + -
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Residues in contact with TYR 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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22A ALA 3.0 7.4 + - - +
23A CYS* 3.2 7.9 - - - -
24A LEU* 2.8 27.2 + - - +
59A PRO* 3.4 38.1 - - - +
60A GLY* 3.4 13.6 + - - -
63A ALA* 3.8 16.4 - - + -
77A LEU* 3.7 28.3 - - + -
78A GLY 3.9 9.9 - - - -
79A ARG 3.5 7.9 - - - -
80A LEU* 3.7 39.3 - - + +
81A LEU* 5.2 0.2 - - - -
94A TYR* 3.9 23.5 - - + -
95A VAL* 1.3 80.0 - - - +
97A VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LEU* 3.5 10.1 - - + -
26A PHE* 4.0 25.6 - - + -
31A GLU* 4.6 3.1 - - - +
77A LEU* 4.0 3.8 - - - +
78A GLY* 2.8 28.7 + - - -
79A ARG* 3.1 56.1 + - + +
81A LEU* 4.9 7.9 - - + -
96A TYR* 1.3 76.9 - - - +
98A LEU* 1.3 61.8 + - - +
143A LEU* 4.0 20.9 - - + -
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Residues in contact with LEU 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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23A CYS* 3.4 16.6 - - - -
24A LEU 3.0 8.1 + - - +
25A CYS* 3.5 13.9 - - - -
26A PHE* 2.9 30.5 + - - -
63A ALA 6.2 0.2 - - - -
64A VAL* 4.8 8.5 - - + -
67A VAL* 4.4 19.5 - - + -
73A VAL* 4.9 4.0 - - + -
74A LYS 4.8 1.3 - - - -
75A GLY* 4.0 27.1 - - - +
76A LYS 3.6 11.2 - - - +
77A LEU* 4.2 19.1 - - + +
78A GLY* 4.3 0.4 - - - +
97A VAL* 1.3 77.6 - - - +
99A THR* 1.3 77.5 + - - +
100A VAL* 3.8 16.6 - - + +
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Residues in contact with THR 99 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A PHE* 3.9 5.4 - - - +
27A ARG 4.9 0.9 - - - +
28A SER* 4.4 27.4 + - - -
29A GLU* 4.6 10.6 - - + +
75A GLY* 3.1 1.4 - - - -
76A LYS* 2.9 44.2 + - - -
98A LEU* 1.3 74.3 - - - +
100A VAL* 1.3 71.8 + - - +
101A THR* 3.5 7.3 + - + +
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Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A CYS* 3.7 28.0 - - + -
26A PHE 3.1 19.0 + - - +
27A ARG* 4.4 8.9 - - - +
35A LEU* 5.0 0.7 - - + -
73A VAL* 4.2 25.1 - - + -
74A LYS 3.9 10.3 - - - +
98A LEU* 4.0 7.4 - - + -
99A THR* 1.3 77.5 - - - +
101A THR* 1.3 64.2 + - - +
102A GLU 4.1 10.8 - - - +
103A ILE* 5.0 3.1 - - + +
119A TRP* 3.8 25.4 - - + -
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Residues in contact with THR 101 (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 LYS* 2.9 16.9 + - - +
75A GLY* 3.4 10.8 - - - -
76A LYS* 4.6 7.2 - - + +
99A THR* 3.5 15.0 + - + +
100A VAL* 1.3 80.4 - - - +
102A GLU* 1.3 64.8 + - - +
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Residues in contact with GLU 102 (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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73A VAL* 3.4 5.2 - - - +
74A LYS* 3.0 38.8 + - + +
100A VAL* 4.1 4.9 - - - +
101A THR* 1.3 85.4 + - - +
103A ILE* 1.3 60.7 + - - +
104A LEU* 4.5 12.5 - - + +
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Residues in contact with ILE 103 (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 GLY 3.9 4.0 - - - -
73A VAL* 4.5 8.1 - - + -
100A VAL* 5.0 3.8 - - + +
102A GLU* 1.3 74.0 - - - +
104A LEU* 1.3 71.0 + - - +
117A ARG* 3.8 15.9 - - - +
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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