Contacts of the helix formed by residues 89 - 102 (chain D) in PDB entry 1V8P
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 89 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B ARG* 6.0 2.2 - - - +
41C ASN* 4.4 4.0 - - - -
44C TRP* 3.3 32.1 - - + -
83D ALA* 4.1 0.9 - - - -
88D LEU* 1.3 77.6 - - - +
90D PHE* 1.3 64.2 + - - +
91D TYR* 3.4 10.7 + - + +
92D ASP* 3.0 33.3 + - - +
93D ALA* 2.9 22.0 + - - +
1004D CL 4.6 11.4 - - + -
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Residues in contact with PHE 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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36C ILE* 4.3 3.6 - - + -
37C TYR* 3.6 42.6 - + + -
40C GLY* 3.7 25.6 - - - -
41C ASN* 3.6 25.0 - - + +
44C TRP* 3.8 11.2 - - + -
76D LEU* 3.8 30.7 - - + -
79D VAL* 3.5 32.5 - - + +
80D LEU* 3.8 21.3 - - + -
83D ALA* 4.2 3.4 - - - -
89D THR* 1.3 73.6 - - - +
91D TYR* 1.3 62.4 + + - +
93D ALA* 4.2 5.2 - - - -
94D SER* 2.9 40.9 + - - -
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Residues in contact with TYR 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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34C LEU* 4.9 3.2 - - + +
37C TYR* 3.5 28.5 - + + -
38C GLU* 3.6 28.5 - - + +
41C ASN* 3.5 36.3 + - + +
91C TYR* 5.2 15.0 - + - -
34D LEU* 3.4 30.5 - - + +
38D GLU* 3.7 18.4 - - - +
89D THR* 3.1 8.6 + - - +
90D PHE* 1.3 81.0 - - - +
92D ASP* 1.3 66.8 + - - +
94D SER* 3.2 11.3 + - - -
95D TYR* 3.3 18.2 - - - -
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Residues in contact with ASP 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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48B ARG* 4.5 9.0 + - - -
8D ASP* 5.1 1.9 - - - +
38D GLU* 5.2 2.9 - - - +
88D LEU* 4.3 14.4 - - + +
89D THR* 3.0 23.4 + - - +
91D TYR* 1.3 80.7 - - - +
93D ALA* 1.3 64.1 + - - +
95D TYR* 3.0 24.6 + - - +
96D ALA 3.2 8.8 + - - -
110D ASP* 3.6 18.8 - - - +
112D GLU* 5.6 0.5 - - - +
113D LEU* 3.8 34.8 - - + +
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Residues in contact with ALA 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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79D VAL* 3.8 10.1 - - + +
82D VAL* 4.2 6.3 - - + +
83D ALA* 3.5 35.0 - - + +
88D LEU* 3.9 13.4 - - + +
89D THR 2.9 19.8 + - - +
90D PHE 3.7 4.0 - - - +
92D ASP* 1.3 77.4 - - - +
94D SER* 1.3 55.8 + - - +
96D ALA* 3.7 2.2 - - - +
97D TYR* 2.9 32.6 + - - +
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Residues in contact with SER 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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37C TYR* 3.7 34.2 - - - -
32D LEU* 4.1 9.4 - - - -
34D LEU* 4.8 0.9 - - - -
74D PRO* 4.4 5.4 - - - -
79D VAL* 3.4 20.9 - - - +
90D PHE* 2.9 24.6 + - - -
91D TYR 3.4 8.9 + - - -
92D ASP 3.1 0.2 - - - -
93D ALA* 1.3 76.0 - - - +
95D TYR* 1.3 62.3 + - - +
97D TYR* 3.9 1.0 - - - +
98D VAL* 3.1 30.8 + - - +
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Residues in contact with TYR 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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6D LEU* 3.6 21.0 - - + +
7D VAL 4.0 3.1 - - - -
8D ASP* 3.6 38.4 - - + -
32D LEU* 3.5 25.4 - - + -
34D LEU* 3.9 9.3 - - + -
35D THR* 2.9 33.5 + - - +
38D GLU* 2.5 32.0 + - - -
91D TYR 3.3 25.6 - - - -
92D ASP* 3.0 16.0 + - - +
94D SER* 1.3 75.1 - - - +
96D ALA* 1.3 65.0 + - - +
99D ALA* 2.9 28.2 + - - +
106D LEU* 4.4 14.1 - - + -
113D LEU* 4.5 6.3 - - + -
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Residues in contact with ALA 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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82D VAL* 4.5 3.4 - - + -
86D ARG* 4.2 14.8 - - - +
88D LEU* 4.1 18.6 - - + -
92D ASP 3.2 8.0 + - - +
93D ALA 3.7 6.7 - - - +
95D TYR* 1.3 78.7 - - - +
97D TYR* 1.3 64.4 + - - +
99D ALA* 3.7 0.5 - - - +
100D GLU* 3.0 31.5 + - - +
106D LEU* 4.7 0.4 - - - +
113D LEU* 4.2 2.1 - - + +
117D THR* 3.4 31.6 - - - +
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Residues in contact with TYR 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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74D PRO* 3.7 20.0 - - + -
75D PRO* 3.9 22.0 - - + +
78D GLU* 3.5 38.5 + - + +
79D VAL* 4.2 12.3 - - + -
81D ARG* 4.8 6.7 - - - -
82D VAL* 4.0 27.7 - - + +
86D ARG* 6.2 0.9 - - - +
93D ALA 2.9 18.1 + - - +
94D SER 3.9 2.5 - - - +
96D ALA* 1.3 77.2 - - - +
98D VAL* 1.3 60.6 + - + +
100D GLU* 4.3 2.0 - - - +
101D SER* 2.8 58.7 + - - -
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Residues in contact with VAL 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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6D LEU* 3.9 14.1 - - + -
32D LEU* 4.1 10.5 - - + -
71D LEU* 3.7 31.0 - - + -
72D GLU 4.9 3.4 - - - +
74D PRO* 3.2 42.0 - - + -
94D SER 3.1 11.1 + - - +
97D TYR* 1.3 80.1 - - + +
99D ALA* 1.3 59.9 + - - +
101D SER* 3.8 5.6 - - - -
102D SER* 2.8 42.9 + - - +
104D LEU* 5.3 0.7 - - + -
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Residues in contact with ALA 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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6D LEU* 4.0 8.9 - - + +
95D TYR 2.9 20.1 + - - +
96D ALA 3.7 2.5 - - - +
98D VAL* 1.3 78.0 - - - +
100D GLU* 1.3 62.9 + - - +
103D GLY 3.0 3.5 + - - -
104D LEU* 2.7 48.2 + - - +
106D LEU* 3.7 29.8 - - + +
117D THR* 4.5 4.9 - - + -
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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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86D ARG* 2.8 45.2 + - - -
96D ALA 3.0 17.9 + - - +
97D TYR* 4.3 2.2 - - - +
99D ALA* 1.3 76.2 - - - +
101D SER* 1.3 61.4 + - - +
103D GLY* 3.0 14.1 + - - -
104D LEU 5.1 0.7 - - - -
117D THR* 3.5 7.1 - - + -
118D LYS* 2.9 63.3 + - + +
128F VAL* 4.2 23.7 - - + +
132F ALA* 4.0 5.7 - - - +
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Residues in contact with SER 101 (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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97D TYR* 2.8 53.9 + - - -
98D VAL* 3.6 5.0 + - - -
100D GLU* 1.3 76.4 - - - +
102D SER* 1.3 61.0 + - - +
103D GLY 3.3 0.7 - - - -
132F ALA* 3.1 20.1 - - - +
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Residues in contact with SER 102 (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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71D LEU* 5.3 2.0 - - - +
98D VAL* 2.8 33.0 + - - +
101D SER* 1.3 80.5 + - - +
103D GLY* 1.3 66.3 + - - +
104D LEU* 3.2 25.0 + - - +
132F ALA* 4.3 4.2 - - - +
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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