Contacts of the strand formed by residues 54 - 69 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LEU* 5.3 2.2 - - - -
18D LEU* 3.5 31.9 - - + -
20D GLU* 4.3 14.4 + - - +
52D ILE 3.7 10.3 - - - +
53D PRO* 1.3 79.9 - - - +
55D LEU* 1.3 61.8 + - - +
87D GLN 3.8 0.5 - - - +
88D VAL* 3.6 7.4 - - - +
89D LEU* 2.9 64.2 + - + +
91D PRO* 6.2 0.2 - - + -
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Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU* 4.3 15.0 - - + +
18D LEU 2.9 14.8 + - - +
19D LEU* 3.5 21.2 - - + +
20D GLU* 2.9 27.3 + - - +
32D ILE* 4.5 7.2 - - + -
36D LEU* 4.4 21.8 - - + -
54D THR* 1.3 72.0 - - - +
56D ARG* 1.3 59.6 + - - +
57D ILE* 3.9 13.9 - - + -
86D ALA* 4.5 15.7 - - + -
87D GLN 3.5 17.0 - - - +
88D VAL* 4.0 17.5 - - + -
98D LEU* 4.9 4.9 - - + -
135D LEU* 5.1 10.8 - - + -
136D VAL* 6.4 0.4 - - + -
139D LEU* 5.0 11.0 - - + -
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Residues in contact with ARG 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLU* 2.7 44.6 + - + +
21D SER* 5.8 0.2 - - - -
54D THR* 4.0 1.0 - - - +
55D LEU* 1.3 72.1 - - - +
57D ILE* 1.3 70.1 + - - +
58D ILE* 3.5 10.1 + - - +
86D ALA* 3.4 3.9 - - - +
87D GLN* 2.9 67.1 + - + +
89D LEU* 3.3 32.3 - - + +
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Residues in contact with ILE 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D LEU* 3.8 27.8 - - + -
20D GLU 2.9 11.4 + - - +
21D SER* 3.7 20.1 - - - +
22D SER* 3.5 20.9 + - - +
28D LEU* 4.4 18.6 - - + -
32D ILE* 3.6 31.4 - - + -
55D LEU* 3.9 14.6 - - + -
56D ARG* 1.3 76.1 - - - +
58D ILE* 1.3 64.0 - - - +
59D GLY* 4.0 17.0 - - - +
84D VAL* 5.0 3.4 - - + -
85D GLN 4.0 6.1 - - - +
86D ALA* 4.4 3.4 - - + +
135D LEU* 4.5 10.1 - - + -
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Residues in contact with ILE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D SER* 3.3 18.0 + - - -
56D ARG* 4.3 14.4 - - - +
57D ILE* 1.3 73.2 - - - +
59D GLY* 1.3 61.4 + - - +
85D GLN* 2.9 41.0 + - + +
86D ALA 4.4 0.4 - - - +
87D GLN* 3.4 46.2 - - + +
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Residues in contact with GLY 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D SER* 4.1 9.0 - - - -
57D ILE* 3.5 7.9 - - - +
58D ILE* 1.3 84.2 - - - +
60D SER* 1.3 63.5 + - - -
84D VAL* 3.8 4.3 - - - +
85D GLN* 3.1 28.4 + - - +
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Residues in contact with SER 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D LEU* 3.7 27.4 - - - +
59D GLY* 1.3 75.2 - - - -
61D SER* 1.3 63.4 + - - +
62D GLU* 5.9 0.7 - - - +
82D LEU* 4.3 8.1 - - - +
83D HIS 3.2 14.1 - - - -
84D VAL* 4.1 4.7 - - - -
85D GLN 5.0 0.2 - - - +
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Residues in contact with SER 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D SER* 1.3 75.9 - - - +
62D GLU* 1.3 67.7 + - - +
63D SER* 5.6 0.4 - - - -
82D LEU* 3.4 4.0 - - - +
83D HIS* 2.9 58.6 + - - +
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Residues in contact with GLU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D SER* 5.9 1.1 - - - +
61D SER* 1.3 79.6 - - - +
63D SER* 1.3 68.4 + - - +
81D VAL 3.4 6.5 - - - +
82D LEU* 4.0 17.9 - - + +
124D ARG* 3.4 31.3 + - - +
128D ARG* 3.4 25.8 + - - +
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Residues in contact with SER 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553C GLN* 3.9 20.9 - - - -
61D SER* 5.6 0.3 - - - -
62D GLU* 1.3 80.6 + - - +
64D GLN* 1.3 63.9 + - - +
65D GLU* 5.6 1.3 - - - -
79D GLN 4.2 0.4 - - - -
80D LEU* 3.4 6.4 - - - +
81D VAL* 2.9 37.0 + - - +
83D HIS* 3.4 20.0 + - - -
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Residues in contact with GLN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C TYR* 5.9 0.6 + - - -
63D SER* 1.3 79.1 - - - +
65D GLU* 1.3 78.7 + - - +
78D ASN* 4.0 22.4 - - + +
79D GLN 3.2 7.2 - - - +
80D LEU* 3.6 23.1 - - + +
106D PHE* 3.8 21.8 - - - -
120D ALA* 5.9 0.9 - - - +
124D ARG* 4.2 12.8 + - - -
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Residues in contact with GLU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546C ASN* 4.7 9.9 + - - +
551C PRO* 3.3 33.8 - - + +
552C TYR 6.0 0.4 - - - +
553C GLN* 3.2 35.8 + - - +
63D SER* 5.6 1.1 - - - -
64D GLN* 1.3 85.8 + - - +
66D THR* 1.3 66.2 + - - +
67D VAL* 3.7 0.4 + - - -
78D ASN* 3.5 5.7 - - - -
79D GLN* 2.9 33.6 + - - +
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Residues in contact with THR 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C THR* 3.8 11.1 + - - +
126C ASP* 5.5 0.7 + - - -
549C ILE 3.8 11.7 - - - +
550C LEU* 3.6 26.1 - - + +
551C PRO* 3.9 8.0 - - - +
65D GLU* 1.3 77.5 + - - +
67D VAL* 1.3 60.1 - - - +
68D SER 3.3 30.1 - - - +
69D ILE* 4.0 7.2 - - + -
75D ALA* 3.8 20.7 - - + +
77D GLU 3.6 5.2 - - - +
78D ASN* 3.0 16.6 + - - -
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429C ASN* 5.3 0.7 + - - -
431C ARG* 3.6 30.6 - - - +
456C GLN* 2.8 20.4 + - - -
476C TYR* 5.1 2.3 - - - -
550C LEU* 3.5 7.6 - - - +
551C PRO 6.2 0.2 - - - +
553C GLN* 4.7 6.5 - - + +
65D GLU 3.7 1.5 + - - +
66D THR* 1.3 78.2 - - - +
68D SER* 1.3 61.1 + - - +
77D GLU* 3.0 31.1 + - + +
78D ASN 4.5 0.7 - - - -
79D GLN* 3.6 44.0 - - + +
105D THR* 4.6 1.1 - - + -
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Residues in contact with SER 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431C ARG* 4.3 2.0 - - - -
454C ILE* 4.2 14.9 - - - +
456C GLN* 3.3 18.8 - - - -
550C LEU* 3.5 4.3 - - - +
66D THR* 3.3 9.0 - - - +
67D VAL* 1.3 83.7 - - - +
69D ILE* 1.3 64.8 + - - +
76D ALA* 2.8 25.7 + - - +
77D GLU* 2.9 40.4 + - - +
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Residues in contact with ILE 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C THR* 3.7 27.8 - - + -
454C ILE* 3.5 14.9 - - - +
456C GLN* 3.6 6.8 + - - +
478C ASP* 6.1 1.4 - - - -
485C ALA* 3.7 31.4 - - + +
508C ILE* 4.1 13.2 - - + -
549C ILE* 3.6 24.0 - - + -
550C LEU* 4.2 10.8 - - + -
66D THR* 4.0 8.7 - - + -
68D SER* 1.3 80.7 - - - +
70D PHE* 1.3 73.0 + - - +
73D GLY* 4.3 6.3 - - - +
74D VAL 3.4 12.8 - - - +
75D ALA* 4.3 0.2 - - - -
76D ALA* 3.8 7.6 - - - +
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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