Contacts of the strand formed by residues 75 - 89 (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 ALA 75 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C THR* 3.0 26.9 + - - +
126C ASP* 5.9 0.2 - - - +
66D THR* 3.8 27.8 - - + +
68D SER 4.0 4.3 - - - -
69D ILE* 4.3 0.7 - - - -
70D PHE* 3.8 9.1 - - - -
73D GLY 3.8 0.8 + - - -
74D VAL* 1.3 81.8 - - + +
76D ALA* 1.3 61.5 + - - +
78D ASN* 4.2 10.1 - - - +
108D ASP* 4.5 22.6 - - - +
110D PRO* 6.1 0.7 - - - +
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Residues in contact with ALA 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C ILE* 3.7 21.3 - - + -
68D SER* 2.8 30.2 + - - +
69D ILE* 3.8 3.8 - - - -
70D PHE* 3.5 26.2 - - + -
74D VAL 3.6 0.8 + - - -
75D ALA* 1.3 75.2 - - - +
77D GLU* 1.3 61.8 + - + +
107D PHE* 3.4 11.7 - - + -
108D ASP* 3.1 27.2 + - - +
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Residues in contact with GLU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C GLN* 5.5 1.8 + - - +
411C LEU* 3.8 12.0 - - - +
431C ARG* 2.5 49.7 + - - +
432C TYR 4.9 1.7 - - - +
433C ALA* 4.4 1.9 - - - +
454C ILE* 4.4 7.0 - - - +
66D THR* 3.6 4.9 - - - +
67D VAL* 3.0 33.3 + - + +
68D SER* 2.9 17.8 + - - +
76D ALA* 1.3 78.5 - - - +
78D ASN* 1.3 68.7 + - - +
105D THR* 5.3 2.9 - - - -
106D PHE 3.6 7.2 - - - +
107D PHE* 3.4 45.1 - - + -
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Residues in contact with ASN 78 (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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64D GLN* 4.0 28.1 - - + +
65D GLU 3.5 5.5 - - - +
66D THR* 3.0 30.8 + - - +
67D VAL* 4.5 2.0 - - - -
75D ALA* 4.2 5.1 - - - +
77D GLU* 1.3 75.8 - - - +
79D GLN* 1.3 61.7 + - - +
105D THR* 3.3 4.2 - - - -
106D PHE* 2.9 46.9 + - + +
108D ASP* 3.3 40.4 + - - +
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Residues in contact with GLN 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C LYS* 5.7 0.9 + - - -
431C ARG* 5.2 3.5 + - - -
553C GLN* 3.5 31.8 + - - +
63D SER 3.7 0.5 - - - +
64D GLN* 3.2 6.2 - - - -
65D GLU 2.9 30.4 + - - +
67D VAL* 3.6 25.3 - - + +
78D ASN* 1.3 74.2 - - - +
80D LEU* 1.3 70.3 + - - +
81D VAL* 3.8 14.0 + - + +
103D PHE* 3.9 24.1 - - + +
104D ARG 3.2 15.7 - - - +
105D THR* 3.8 14.8 - - + +
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Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D SER 3.4 4.9 - - - +
64D GLN* 3.6 40.4 - - + +
78D ASN 4.2 0.2 + - - -
79D GLN* 1.3 72.8 - - - +
81D VAL* 1.3 62.1 + - - +
103D PHE* 3.5 2.9 - - - -
104D ARG* 2.9 34.8 + - + +
106D PHE* 3.5 28.5 - - + -
120D ALA* 4.1 16.6 - - + +
123D LEU* 3.9 29.2 - - + -
124D ARG* 4.4 20.0 - - + +
127D MET* 3.4 17.0 - - + +
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Residues in contact with VAL 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C GLN* 3.9 20.0 - - + +
61D SER 3.8 0.3 - - - +
62D GLU* 3.4 7.4 - - - +
63D SER* 2.9 40.4 + - - +
79D GLN* 3.8 19.1 - - + +
80D LEU* 1.3 81.6 - - - +
82D LEU* 1.3 65.4 + - - +
83D HIS* 3.4 30.3 - - + +
101D ASN* 5.4 0.2 - - + -
102D VAL 3.4 5.6 - - - +
103D PHE* 3.6 36.8 - - + -
127D MET* 3.6 2.5 - - - -
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Residues in contact with LEU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LEU* 5.1 2.9 - - + -
60D SER* 4.3 10.3 - - - +
61D SER 3.4 16.8 - - - +
62D GLU* 4.0 20.0 - - + +
81D VAL* 1.3 74.8 - - - +
83D HIS* 1.3 68.9 + - - +
84D VAL* 3.9 13.0 - - + -
100D VAL 3.5 1.7 - - - +
101D ASN* 3.3 6.2 - - - +
102D VAL* 2.9 38.4 + - + +
127D MET* 3.3 18.6 - - + +
128D ARG* 3.9 41.1 - - + +
131D ALA* 3.9 18.6 - - + -
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Residues in contact with HIS 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C GLN* 5.6 3.5 + - + -
554C SER 5.8 2.9 - - - -
60D SER* 3.2 6.2 - - - -
61D SER* 2.9 56.3 + - - +
63D SER* 3.4 24.7 + - - -
81D VAL* 3.4 26.9 - - + +
82D LEU* 1.3 74.8 - - - +
84D VAL* 1.3 64.1 + - - +
85D GLN 4.3 0.2 - - - -
99D GLN* 5.6 5.8 - - - +
100D VAL 3.6 4.0 - - - -
101D ASN* 3.4 21.0 + - - +
103D PHE* 5.7 1.3 - + - -
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Residues in contact with VAL 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D LEU* 4.2 17.7 - - + -
57D ILE* 5.0 4.9 - - + -
59D GLY 3.8 8.1 - - - +
60D SER* 4.1 9.6 - - - -
82D LEU* 3.9 23.8 - - + -
83D HIS* 1.3 81.2 - - - +
85D GLN* 1.3 68.7 + - - +
86D ALA* 4.8 1.7 - - + +
99D GLN* 3.2 11.6 - - - +
100D VAL* 2.9 49.3 + - + +
101D ASN* 4.6 0.4 + - - -
131D ALA* 4.1 14.1 - - + -
135D LEU* 4.4 22.7 - - + -
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Residues in contact with GLN 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D ILE* 3.8 3.3 - - - +
58D ILE* 2.9 55.0 + - + +
59D GLY* 3.1 19.2 + - - +
60D SER* 5.0 0.2 - - - +
83D HIS 4.3 0.4 - - - -
84D VAL* 1.3 72.1 - - - +
86D ALA* 1.3 67.1 + - - +
97D PRO* 4.6 7.8 - - - +
98D LEU 2.8 24.5 + - - +
99D GLN* 2.9 31.4 - - - +
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Residues in contact with ALA 86 (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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55D LEU* 4.5 8.5 - - + -
56D ARG 3.4 12.1 - - - +
57D ILE* 4.5 5.4 - - + -
58D ILE* 4.3 1.8 - - - +
84D VAL* 4.1 2.2 + - + -
85D GLN* 1.3 79.7 - - - +
87D GLN* 1.3 71.6 + - - +
97D PRO* 3.7 0.2 - - - +
98D LEU* 2.9 34.3 + - + +
135D LEU* 4.0 36.8 - - + -
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Residues in contact with GLN 87 (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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54D THR 3.8 0.9 - - - +
55D LEU* 3.5 6.2 - - - +
56D ARG* 2.9 67.5 + - + +
58D ILE* 3.4 25.6 - - + +
85D GLN* 5.3 0.2 - - - +
86D ALA* 1.3 81.8 - - - +
88D VAL* 1.3 63.3 + - - +
89D LEU* 3.9 11.4 - - + +
95D ILE* 4.1 22.4 - - + +
96D TYR 3.7 4.9 - - - -
97D PRO* 4.4 12.5 - - + +
98D LEU* 4.4 0.7 - - - +
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Residues in contact with VAL 88 (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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14D LEU* 5.7 5.4 - - + -
53D PRO* 5.5 4.5 - - + -
54D THR 3.6 6.5 - - - +
55D LEU* 4.0 11.9 - - + -
87D GLN* 1.3 74.8 - - - +
89D LEU* 1.3 63.5 + - - +
90D ILE* 3.9 14.3 + - + +
94D ASP 4.3 0.9 - - - +
95D ILE* 3.9 1.4 - - - -
96D TYR* 2.9 41.1 + - + +
98D LEU* 3.6 30.3 - - + -
139D LEU* 4.3 10.1 - - + -
142D VAL* 3.6 39.3 - - + -
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Residues in contact with LEU 89 (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* 4.7 0.9 - - - +
53D PRO* 3.3 3.5 - - - +
54D THR* 2.9 56.6 + - + +
56D ARG* 3.3 40.2 - - + +
87D GLN* 3.9 30.5 - - + +
88D VAL* 1.3 74.3 - - - +
90D ILE* 1.3 62.5 + - - +
91D PRO* 3.9 2.0 - - - +
95D ILE* 3.6 30.5 - - + -
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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