Contacts of the helix formed by residues 86 - 101 (chain D) in PDB entry 1U5T
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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200A SER* 5.1 6.1 - - - -
14D TYR 4.4 3.5 + - - -
16D ARG* 6.3 1.6 - - - -
85D VAL* 1.3 80.8 - - - +
87D GLN* 1.3 54.6 + - - +
88D VAL* 3.0 20.4 + - - +
89D PHE* 2.7 17.1 + - - +
90D ILE* 2.6 40.5 + - - +
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Residues in contact with GLN 87 (chain D).
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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196A VAL* 4.5 27.8 - - + -
48D VAL* 3.2 30.6 - - - +
49D ASP* 4.7 14.8 - - - +
85D VAL 4.3 0.4 + - - -
86D SER* 1.3 72.5 + - - +
88D VAL* 1.3 64.9 + - - +
90D ILE* 2.7 27.4 + - - +
91D ASP* 2.8 29.0 + - - +
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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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196A VAL* 3.9 23.5 - - + +
197A ARG* 4.7 17.5 - - + -
200A SER* 4.2 17.5 - - - +
16D ARG* 6.5 1.1 - - - -
86D SER* 3.0 9.8 + - - +
87D GLN* 1.3 75.2 - - + +
89D PHE* 1.3 67.1 + - - +
91D ASP* 3.7 9.0 + - + +
92D GLU* 3.0 28.3 + - + +
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Residues in contact with PHE 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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13D LEU 4.8 0.9 - - - -
14D TYR 5.1 2.7 - - - -
15D THR 4.2 1.3 - - - -
16D ARG* 3.4 39.9 - - + -
23D ARG* 4.6 4.0 - - + -
26D GLN* 3.3 37.7 - - + -
27D ILE* 3.7 29.6 - - + -
30D TRP* 4.7 7.9 - + - -
85D VAL* 3.8 16.2 - - + -
86D SER* 2.7 23.4 + - - +
88D VAL* 1.3 72.9 - - - +
90D ILE* 1.3 70.6 + - - +
92D GLU* 2.5 31.2 + - + +
93D ILE* 2.6 32.6 + - + -
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Residues in contact with ILE 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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48D VAL* 3.6 13.0 - - + +
76D PHE* 3.1 33.7 - - + -
85D VAL* 3.3 23.9 - - + +
86D SER 2.6 49.1 + - - +
87D GLN* 2.7 20.1 + - - +
89D PHE* 1.3 73.5 - - - +
91D ASP* 1.3 50.6 - - - +
93D ILE* 2.3 36.7 + - + -
94D TRP* 2.5 52.1 + - + +
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Residues in contact with ASP 91 (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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196A VAL* 5.9 1.9 - - - +
48D VAL* 3.5 13.3 - - - +
87D GLN* 2.8 41.6 + - - +
88D VAL* 3.8 7.0 - - - +
90D ILE* 1.3 70.6 - - - +
92D GLU* 1.3 62.6 - - - +
94D TRP* 3.5 9.6 - - - +
95D SER* 3.0 24.8 + - - -
121D TYR* 5.6 0.4 - - - -
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Residues in contact with GLU 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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16D ARG* 4.7 0.7 - - - +
23D ARG* 3.3 45.4 + - - +
27D ILE* 4.7 8.7 - - + +
88D VAL* 3.0 21.4 + - + +
89D PHE* 2.5 34.5 + - + +
91D ASP* 1.3 71.1 - - - +
93D ILE* 1.3 65.6 + - - +
94D TRP 3.3 0.2 + - - -
95D SER* 3.4 5.4 + - - -
96D GLN* 3.3 19.9 + - - +
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Residues in contact with ILE 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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27D ILE* 4.1 14.4 - - + +
30D TRP* 3.0 56.8 - - + +
31D ILE* 4.6 19.9 - - + +
34D ILE* 5.1 4.5 - - + -
76D PHE* 4.9 13.9 - - + -
85D VAL* 5.3 2.0 - - + -
89D PHE* 2.6 37.2 + - + +
90D ILE* 2.3 28.3 + - - +
92D GLU* 1.3 71.5 - - - +
94D TRP* 1.3 70.9 + - + +
96D GLN* 3.4 4.2 + - - +
97D MET* 3.2 13.5 + - + +
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Residues in contact with TRP 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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34D ILE* 4.0 5.6 - - + -
46D MET* 3.1 36.1 - - + -
47D SER 3.6 11.7 - - - -
48D VAL* 3.3 22.0 - - + +
76D PHE* 5.0 5.6 - + - -
90D ILE* 2.5 43.5 + - + +
91D ASP* 3.5 11.9 - - - +
93D ILE* 1.3 71.7 - - + +
95D SER* 1.3 53.9 + - - +
97D MET* 2.4 72.5 + - + +
98D THR* 2.9 10.2 + - - -
103D CYS* 3.9 15.0 - - + -
121D TYR* 3.3 61.5 - + + +
123D ILE* 4.7 1.1 - - + -
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Residues in contact with SER 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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91D ASP 3.0 15.5 + - - -
92D GLU* 3.4 6.9 + - - -
94D TRP* 1.3 75.5 - - - +
96D GLN* 1.3 59.3 + - - +
98D THR* 2.9 36.3 + - - +
99D LYS* 3.0 10.0 + - - +
121D TYR* 5.0 0.6 + - - -
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Residues in contact with GLN 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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24D ARG* 6.0 5.3 - - + +
27D ILE* 4.3 28.7 - - + -
31D ILE* 4.7 1.6 - - + -
92D GLU 3.3 8.7 + - - +
93D ILE 4.1 6.1 - - - +
94D TRP 2.8 3.0 + - - -
95D SER* 1.3 77.8 + - - +
97D MET* 1.3 59.8 + - - +
99D LYS* 4.0 31.0 + - - +
100D GLU* 3.1 50.3 + - - +
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Residues in contact with MET 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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31D ILE* 3.6 42.6 - - + +
34D ILE* 3.3 31.2 - - + -
35D SER* 5.1 3.4 - - - -
93D ILE* 3.2 7.5 + - + +
94D TRP* 2.4 70.8 + - + +
96D GLN* 1.3 67.7 - - - +
98D THR* 1.3 68.4 + - - +
100D GLU* 3.2 5.1 + - + +
101D GLY 2.9 13.2 + - - -
102D LYS* 3.4 31.5 + - + +
103D CYS* 3.3 17.0 - - + -
123D ILE* 5.7 1.6 - - + -
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Residues in contact with THR 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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94D TRP 2.9 4.8 + - - -
95D SER* 2.9 23.6 - - - +
97D MET* 1.3 73.0 - - - +
99D LYS* 1.3 70.0 + - + +
101D GLY* 2.4 35.3 + - - -
103D CYS* 3.2 21.2 - - - +
104D LEU* 5.9 1.5 - - + +
105D PRO* 4.9 9.2 - - - +
112D ARG* 6.1 2.5 - - - +
121D TYR* 4.2 13.5 + - - -
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Residues in contact with LYS 99 (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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95D SER* 3.0 10.2 + - - +
96D GLN* 4.0 28.3 + - - +
98D THR* 1.3 85.9 - - + +
100D GLU* 1.3 60.1 + - + +
101D GLY* 2.9 6.1 + - - -
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Residues in contact with GLU 100 (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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27D ILE* 5.5 0.5 - - - +
28D SER* 5.4 5.4 + - - -
31D ILE* 4.3 12.4 - - + +
96D GLN* 3.1 48.0 + - - +
97D MET* 3.2 7.1 + - - +
98D THR 3.0 1.2 + - - -
99D LYS* 1.3 76.9 - - + +
101D GLY* 1.3 64.5 + - - +
102D LYS* 4.4 8.6 - - + +
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Residues in contact with GLY 101 (chain D).
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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97D MET 2.9 1.2 + - - -
98D THR 2.4 28.2 + - - -
99D LYS 2.8 3.8 + - - -
100D GLU* 1.3 69.6 - - - +
102D LYS* 1.3 68.8 + - - +
103D CYS 4.9 2.7 - - - -
124D LEU* 4.6 7.1 - - - +
127D SER* 5.6 4.7 - - - -
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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