Contacts of the strand formed by residues 86 - 98 (chain D) in PDB entry 1QD6
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 SER 86 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B LEU* 3.4 9.2 - - - +
79D ARG* 3.9 0.2 - - - -
80D GLY 3.0 20.4 + - - -
81D ILE* 3.7 3.2 + - - -
82D LEU* 2.9 28.9 + - - -
83D GLY 2.8 18.5 + - - -
84D PRO 4.7 0.3 - - - +
85D ASN* 1.3 79.6 - - - +
87D VAL* 1.3 64.8 + - - +
120D LEU* 5.7 0.9 - - - -
121D GLY 3.1 6.3 - - - -
122D PHE* 3.4 33.4 - - - -
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Residues in contact with VAL 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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19B ILE* 3.8 27.8 - - + -
22B MET* 4.7 15.7 - - + -
23B LEU* 4.0 8.7 - - + -
76D PRO* 4.3 16.8 - - + -
78D TRP 3.5 10.1 - - - +
79D ARG* 4.2 16.8 - - + -
81D ILE* 4.2 4.5 - - - -
86D SER* 1.3 79.0 - - - +
88D LEU* 1.3 76.0 + - - +
89D GLY* 3.6 1.6 + - - +
119D PHE* 4.9 2.0 - - + -
120D LEU* 3.4 2.9 - - - -
121D GLY* 2.7 50.0 + - - +
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Residues in contact with LEU 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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77D LEU* 3.0 34.2 + - + +
78D TRP* 2.9 43.0 + - + +
81D ILE* 3.7 28.8 - - + +
87D VAL* 1.3 75.3 - - - +
89D GLY* 1.3 62.7 + - - +
118D LEU* 3.9 24.9 - - + -
119D PHE 3.4 15.0 - - - +
120D LEU* 4.2 8.5 - - + -
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Residues in contact with GLY 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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22B MET* 5.1 1.1 - - - -
75D PHE 3.5 10.5 - - - -
76D PRO* 4.6 1.8 - - - -
77D LEU* 4.1 6.1 - - - -
87D VAL* 3.6 4.4 + - - -
88D LEU* 1.3 76.2 - - - +
90D ALA* 1.3 61.7 + - - -
118D LEU* 3.4 9.0 - - - +
119D PHE* 2.9 50.8 + - - +
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Residues in contact with ALA 90 (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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74D ALA* 3.4 2.6 - - - -
75D PHE* 2.6 56.1 + - + +
77D LEU* 4.0 17.3 - - + -
89D GLY* 1.3 76.2 - - - +
91D SER* 1.3 59.0 + - - +
117D GLN 3.2 13.5 - - - +
118D LEU* 4.6 3.8 - - + -
119D PHE* 3.8 7.0 - - - -
270D HDS 5.5 2.2 - - + -
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Residues in contact with SER 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D TYR* 3.7 30.2 - - - -
73D LEU 3.2 13.9 - - - -
74D ALA* 4.4 0.2 - - - -
75D PHE* 4.0 5.8 - - - -
90D ALA* 1.3 76.4 - - - +
92D TYR* 1.3 63.0 + - - +
93D THR* 5.1 0.5 + - - -
115D GLU 4.4 0.9 + - - -
116D PRO* 3.4 4.2 - - - +
117D GLN* 2.9 60.0 + - - +
119D PHE* 3.8 4.4 - - - -
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Residues in contact with TYR 92 (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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69C PHE* 3.9 11.6 - + - -
71C LEU* 3.6 30.5 - - + -
71D LEU* 5.3 3.8 - - + -
72D SER* 3.3 3.5 - - - -
73D LEU* 3.0 33.8 + - + -
75D PHE* 3.9 19.3 - + + -
91D SER* 1.3 76.4 - - - +
93D THR* 1.3 64.2 + - - +
94D GLN* 2.7 39.5 + - + +
114D TYR* 3.1 20.9 - - + -
115D GLU 3.6 17.3 - - - -
116D PRO* 4.2 9.4 - - + -
270D HDS 3.4 47.8 - - + -
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Residues in contact with THR 93 (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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35D TYR* 4.1 13.2 - - - -
36D ASP* 4.2 6.3 - - + +
70D GLN* 3.9 21.3 - - + +
71D LEU 3.4 4.9 - - - +
72D SER* 2.8 20.8 + - - -
91D SER* 5.1 0.7 + - - -
92D TYR* 1.3 76.8 + - - +
94D GLN* 1.3 63.1 + - - +
95D LYS* 3.8 27.1 - - + +
113D ASN 3.8 1.2 - - - +
114D TYR 3.7 0.2 - - - -
115D GLU* 2.7 56.6 + - - +
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Residues in contact with GLN 94 (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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94C GLN* 2.8 41.2 + - - -
114C TYR* 5.0 3.0 - - - -
69D PHE* 3.7 6.6 - - - +
70D GLN* 3.1 7.3 - - - +
71D LEU* 2.9 51.8 + - + +
92D TYR* 2.7 38.9 + - + +
93D THR* 1.3 75.6 - - - +
95D LYS* 1.3 64.1 + - - +
96D SER* 3.4 18.5 + - - +
112D THR* 3.6 22.1 - - + +
113D ASN 3.3 4.3 - - - +
114D TYR* 4.1 3.5 - - + -
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Residues in contact with LYS 95 (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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36D ASP* 4.7 1.4 + - - -
39D TYR* 5.5 1.6 - - - +
68D LYS* 5.3 8.3 - - + +
69D PHE 3.4 6.5 - - - +
70D GLN* 2.7 35.2 + - + +
93D THR* 3.8 14.7 - - + +
94D GLN* 1.3 76.6 - - - +
96D SER* 1.3 61.4 + - - +
97D TRP* 3.5 32.2 - - + -
112D THR* 3.2 4.5 - - - +
113D ASN* 2.7 47.7 + - + +
115D GLU* 4.3 16.1 + - - -
211D LYS* 3.8 18.7 - - - +
247D GLU 4.7 6.5 - - - +
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Residues in contact with SER 96 (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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114C TYR* 5.1 0.3 - - - -
67D VAL 3.5 0.7 - - - +
68D LYS* 3.3 7.3 - - - +
69D PHE* 2.9 45.7 + - - -
94D GLN* 3.4 14.9 + - - -
95D LYS* 1.3 72.2 - - - +
97D TRP* 1.3 67.4 + - - +
98D TRP 4.1 0.4 - - - -
109D PHE* 3.4 26.3 - - - -
111D GLU 3.5 4.3 - - - -
112D THR* 3.2 24.6 + - - +
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Residues in contact with TRP 97 (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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66D GLU* 3.7 13.2 - - + +
67D VAL 3.4 4.3 - - - -
68D LYS* 3.4 38.0 - - + +
95D LYS* 3.5 40.2 - - + -
96D SER* 1.3 74.4 - - - +
98D TRP* 1.3 59.9 + - - +
109D PHE* 3.6 4.2 - - - +
110D ARG* 2.9 56.2 + - - +
111D GLU* 2.8 36.4 + - + +
113D ASN* 4.0 8.1 - - - -
247D GLU* 3.0 44.3 + - - -
248D SER* 3.5 25.1 - - - -
258D ARG* 3.8 15.7 - - - -
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Residues in contact with TRP 98 (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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142C HIS* 5.5 2.7 - + - -
270C HDS 3.5 66.0 + - + +
40D LEU* 6.0 0.7 - - + -
66D GLU* 3.4 5.3 - - - +
67D VAL* 2.9 61.3 + - + +
69D PHE* 5.1 2.9 - + + -
97D TRP* 1.3 72.5 - - - +
99D GLN* 1.3 59.0 + - - +
100D LEU* 2.8 57.1 + - + +
107D SER* 3.1 33.0 + - - -
108D PRO 3.6 2.5 - - - -
109D PHE* 3.6 33.4 - + + +
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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