Contacts of the strand formed by residues 54 - 69 (chain H) in PDB entry 5IXM
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 THR 54 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H LEU* 5.1 2.5 - - - -
18H LEU* 3.5 37.9 - - + +
20H GLU* 4.9 5.5 + - - +
50H LYS* 5.8 6.5 - - + -
52H ILE 3.9 7.2 - - - +
53H PRO* 1.3 77.0 - - - +
55H LEU* 1.3 61.5 + - - +
56H ARG* 4.8 1.6 - - - +
87H GLN 3.7 0.2 - - - +
88H VAL* 3.4 9.2 - - - +
89H LEU* 2.9 63.5 + - + +
91H PRO* 5.8 1.8 - - + -
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Residues in contact with LEU 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H LEU* 4.4 15.6 - - + +
18H LEU 2.9 15.4 + - - +
19H LEU* 3.4 23.9 - - + +
20H GLU* 2.9 28.1 + - - +
32H ILE* 4.4 8.7 - - + -
36H LEU* 4.1 25.4 - - + -
54H THR* 1.3 73.6 - - - +
56H ARG* 1.3 59.5 + - - +
57H ILE* 4.1 5.6 - - + -
86H ALA* 4.5 9.6 - - + -
87H GLN 3.5 16.6 - - - +
88H VAL* 3.9 18.6 - - + -
135H LEU* 4.2 27.8 - - + -
139H LEU* 5.2 5.6 - - + -
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Residues in contact with ARG 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20H GLU* 3.3 33.2 + - + +
21H SER* 5.7 0.2 - - - -
54H THR* 4.0 0.8 - - - +
55H LEU* 1.3 71.5 - - - +
57H ILE* 1.3 72.4 + - - +
58H ILE* 3.5 11.5 + - + +
86H ALA* 3.3 3.6 - - - -
87H GLN* 2.9 66.7 + - + +
89H LEU* 3.5 37.6 - - + +
95H ILE* 6.0 0.2 - - - +
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Residues in contact with ILE 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H LEU* 3.7 27.4 - - + -
20H GLU 2.9 11.5 + - - +
21H SER* 3.6 19.7 - - - +
22H SER* 3.2 22.4 + - - +
28H LEU* 4.6 16.8 - - + -
29H ALA* 6.2 1.3 - - + -
32H ILE* 3.5 32.1 - - + -
55H LEU* 4.1 13.9 - - + -
56H ARG* 1.3 76.6 - - - +
58H ILE* 1.3 62.6 + - - +
59H GLY* 4.0 19.7 - - - +
84H VAL* 4.9 4.0 - - + -
85H GLN 4.0 4.5 - - - +
86H ALA* 4.5 8.7 - - + -
135H LEU* 4.8 3.1 - - + -
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Residues in contact with ILE 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H SER* 3.0 22.3 + - - -
56H ARG* 3.6 15.0 - - + +
57H ILE* 1.3 71.4 - - - +
59H GLY* 1.3 60.3 + - - +
85H GLN* 2.9 35.3 + - + +
86H ALA* 3.5 24.9 - - - +
87H GLN* 3.5 29.8 - - + +
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Residues in contact with GLY 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H SER* 3.8 9.9 - - - -
57H ILE* 3.5 8.2 - - - +
58H ILE* 1.3 83.6 - - - +
60H SER* 1.3 62.5 + - - -
84H VAL* 3.8 4.2 - - - +
85H GLN* 3.3 26.9 + - - +
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Residues in contact with SER 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H LEU* 3.6 29.6 - - - +
59H GLY* 1.3 75.9 - - - -
61H SER* 1.3 62.3 + - - +
62H GLU* 6.0 0.5 - - - +
82H LEU* 4.2 8.6 - - - +
83H HIS 3.2 13.9 - - - -
84H VAL* 4.0 4.0 - - - -
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Residues in contact with SER 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60H SER* 1.3 76.0 - - - +
62H GLU* 1.3 67.0 + - - +
63H SER* 5.5 0.9 - - - -
81H VAL 3.8 0.2 - - - +
82H LEU* 3.5 6.0 - - - +
83H HIS* 2.9 55.4 + - - +
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Residues in contact with GLU 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60H SER* 5.9 1.1 - - - +
61H SER* 1.3 79.7 - - - +
63H SER* 1.3 67.6 + - - +
81H VAL 3.3 7.0 - - - +
82H LEU* 4.1 17.0 - - + +
124H ARG* 3.4 32.5 + - - +
128H ARG* 3.6 23.0 + - - +
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Residues in contact with SER 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553G GLN* 4.0 16.8 - - - -
61H SER* 5.3 1.0 + - - -
62H GLU* 1.3 79.6 + - - +
64H GLN* 1.3 65.0 + - - +
65H GLU* 5.6 1.6 - - - -
79H GLN 4.4 0.4 - - - -
80H LEU* 3.5 5.4 - - - +
81H VAL* 3.0 38.6 + - - +
83H HIS* 4.0 17.3 + - - -
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Residues in contact with GLN 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G TYR* 6.0 0.2 + - - -
63H SER* 1.3 78.6 - - - +
65H GLU* 1.3 81.5 + - - +
78H ASN* 4.2 17.2 - - + +
79H GLN 3.4 7.4 - - - +
80H LEU* 3.5 23.4 - - + +
106H PHE* 3.8 23.6 - - - -
120H ALA* 5.8 0.7 - - - +
124H ARG* 3.6 16.1 + - - +
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Residues in contact with GLU 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546G ASN* 4.8 9.5 + - - +
551G PRO* 3.3 32.7 - - + +
553G GLN* 3.2 38.7 - - + +
63H SER* 5.6 1.3 - - - -
64H GLN* 1.3 85.6 + - - +
66H THR* 1.3 65.0 + - - +
67H VAL* 3.8 0.4 + - + -
78H ASN* 3.6 5.9 - - - +
79H GLN* 2.9 32.6 + - - +
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Residues in contact with THR 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G THR* 4.0 11.3 + - - -
126G ASP* 5.6 0.5 + - - -
549G ILE 3.8 15.9 + - - +
550G LEU* 3.3 25.8 - - + +
551G PRO* 4.0 6.0 - - - +
65H GLU* 1.3 76.1 + - - +
67H VAL* 1.3 65.0 + - - +
68H SER 3.3 25.4 - - - +
69H ILE* 4.2 5.6 - - + -
75H ALA* 3.8 23.3 - - + +
77H GLU 3.7 5.2 - - - +
78H ASN* 3.0 15.7 + - - -
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Residues in contact with VAL 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431G ARG* 3.6 30.2 - - - +
456G GLN* 2.9 19.4 + - - -
476G TYR* 5.1 2.6 - - - -
550G LEU* 3.6 8.2 - - - +
553G GLN* 4.3 6.1 - - + +
65H GLU 4.2 1.6 - - - +
66H THR* 1.3 78.1 - - - +
68H SER* 1.3 60.5 + - - +
77H GLU* 3.0 31.2 + - + +
78H ASN 4.4 6.1 - - - +
79H GLN* 3.6 37.9 - - + +
105H THR* 4.8 1.1 - - + -
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Residues in contact with SER 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431G ARG* 4.4 1.8 - - - -
454G ILE* 4.3 12.9 - - - +
456G GLN* 3.3 18.8 - - - +
550G LEU* 3.7 4.7 - - - +
66H THR* 3.3 9.2 - - - +
67H VAL* 1.3 82.7 - - - +
69H ILE* 1.3 59.1 + - - +
76H ALA* 2.7 32.8 + - - +
77H GLU* 2.9 45.1 + - - +
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Residues in contact with ILE 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G THR* 3.8 25.8 - - + -
454G ILE* 3.6 13.9 - - - +
456G GLN* 3.5 8.0 + - - +
485G ALA* 3.6 44.8 - - + +
508G ILE* 4.2 11.9 - - + -
549G ILE* 3.7 17.9 - - + -
550G LEU* 4.4 7.6 - - + -
66H THR* 4.2 7.4 - - + -
68H SER* 1.3 79.9 - - - +
70H PHE* 1.3 71.0 + - - +
73H GLY* 3.9 6.1 - - - +
74H VAL 3.4 15.5 - - - +
76H ALA* 3.9 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