Contacts of the helix formed by residues 92 - 106 (chain D) in PDB entry 4BSX
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 VAL 92 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D SER* 6.2 0.4 - - - -
8D LEU* 4.7 12.8 - - + +
69D VAL* 4.2 20.9 - - + -
72D LEU* 4.0 24.9 - - + -
90D PRO* 3.3 21.3 + - + +
91D ASP* 1.3 74.3 + - - +
93D SER* 1.3 60.7 + - - +
94D TRP 3.2 2.9 + - - -
95D ALA* 3.3 3.9 + - - +
96D VAL* 2.8 47.4 + - + +
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Residues in contact with SER 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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91D ASP* 3.2 24.6 + - - -
92D VAL* 1.3 80.6 - - - +
94D TRP* 1.3 59.2 + - - +
96D VAL* 3.4 7.5 + - - +
97D ALA* 2.9 27.4 + - - +
117D ALA 4.2 3.2 - - - +
120D GLU* 4.4 5.2 - - - -
121D ALA* 3.4 33.5 + - - +
124D THR* 3.7 12.6 - - - -
125D LEU* 4.4 1.9 - - - +
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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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91D ASP* 5.2 1.7 + - - +
92D VAL 3.3 0.4 - - - -
93D SER* 1.3 77.9 + - - +
95D ALA* 1.3 65.7 + - - +
97D ALA* 3.2 2.4 + - - +
98D ARG* 3.0 50.0 + - - +
118D TYR* 4.5 2.2 - + - -
121D ALA* 4.1 8.3 - - + -
125D LEU* 3.9 33.4 - - + -
128D ARG* 6.3 0.2 - - - -
132D ARG* 3.4 46.2 - - + -
135D GLU* 3.8 17.5 - - + -
136D LEU* 3.4 37.4 - - + +
139D GLU* 3.0 33.9 + - - -
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Residues in contact with ALA 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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42D LEU* 4.6 10.3 - - + -
69D VAL* 3.9 36.8 - - + -
92D VAL* 3.3 8.2 + - + +
94D TRP* 1.3 79.1 - - - +
96D VAL* 1.3 60.4 + - + +
98D ARG* 3.2 11.8 + - - +
99D LEU* 2.9 34.4 + - + +
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Residues in contact with VAL 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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6D PRO* 4.1 7.0 - - + +
7D SER* 4.0 14.8 - - - +
8D LEU* 3.9 29.6 - - + +
92D VAL* 2.8 41.1 + - + +
93D SER* 3.7 7.2 - - - +
94D TRP 3.2 0.2 - - - -
95D ALA* 1.3 78.3 - - + +
97D ALA* 1.3 56.9 + - - +
99D LEU* 3.1 8.4 + - + +
100D TYR* 2.8 53.5 + - + -
117D ALA* 4.5 7.4 - - + -
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Residues in contact with ALA 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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93D SER 2.9 14.6 + - - +
94D TRP* 3.2 11.0 + - - +
96D VAL* 1.3 76.3 - - - +
98D ARG* 1.3 56.7 + - - +
100D TYR* 3.3 2.6 + - - +
101D HIS* 2.9 28.8 + - - +
114D ARG* 4.5 0.5 - - - +
117D ALA* 3.7 23.5 - - - +
118D TYR* 3.6 43.4 - - + +
121D ALA* 4.5 1.6 - - + -
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Residues in contact with ARG 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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38D GLN* 3.4 60.2 - - - +
39D GLY* 4.7 5.4 - - - +
94D TRP* 3.0 40.4 + - - +
95D ALA* 3.2 11.6 + - - +
97D ALA* 1.3 76.9 - - - +
99D LEU* 1.3 64.0 + - - +
101D HIS* 3.1 15.1 + - - +
102D LEU* 3.2 19.9 + - - +
118D TYR* 3.7 4.7 - - - +
132D ARG* 4.6 9.5 - - - +
135D GLU* 4.7 4.8 + - - -
139D GLU* 2.9 42.5 + - - +
143D ARG* 4.1 5.4 - - - +
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Residues in contact with LEU 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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8D LEU* 4.0 14.1 - - + -
11D ALA* 4.9 7.6 - - + -
39D GLY* 3.7 17.3 - - - +
42D LEU* 4.1 15.3 - - + -
43D LEU* 3.7 41.9 - - + +
46D MSE 3.5 31.9 - - + -
69D VAL* 6.3 0.2 - - + -
95D ALA* 2.9 19.0 + - + +
96D VAL* 3.5 13.2 - - + +
98D ARG* 1.3 74.1 - - - +
100D TYR* 1.3 62.4 + - + +
102D LEU* 3.3 7.8 + - - +
103D LEU* 3.0 31.8 + - + +
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Residues in contact with TYR 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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6D PRO* 3.6 13.5 - - + +
7D SER 3.4 27.2 + - - -
10D SER* 3.2 31.4 - - - -
11D ALA* 3.4 16.2 + - + -
14D ILE* 3.7 23.7 - - + +
96D VAL* 2.8 29.9 + - + +
97D ALA 3.9 3.4 - - - +
99D LEU* 1.3 75.3 - - + +
101D HIS* 1.3 65.9 + - - +
103D LEU* 3.8 6.0 - - + +
104D ALA* 2.9 26.0 + - - +
109D CYS* 4.0 11.6 - - - -
113D MSE 3.8 35.2 - - + -
114D ARG* 4.0 17.9 - - - +
117D ALA* 4.3 5.2 - - + -
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Residues in contact with HIS 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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142B ASN* 6.0 2.0 + - - -
36D GLY 4.9 5.2 + - - -
37D CYS* 6.0 1.4 - - - -
97D ALA 2.9 14.7 + - - +
98D ARG 3.1 8.2 + - - +
100D TYR* 1.3 80.3 - - - +
102D LEU* 1.3 78.9 + - + +
104D ALA* 3.5 1.7 + - - +
105D GLU* 3.1 60.1 + - + +
114D ARG* 3.5 32.9 - - + +
118D TYR* 4.3 2.7 - - + -
143D ARG* 3.4 53.4 + - + +
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Residues in contact with LEU 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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30D LEU* 5.3 3.8 - - + -
37D CYS* 4.4 27.6 - - + -
38D GLN 4.0 4.5 - - - +
39D GLY* 3.8 6.5 - - - +
40D GLN* 3.5 41.7 - - + +
43D LEU* 3.6 27.1 - - + -
98D ARG 3.2 16.1 + - - +
99D LEU* 3.3 3.8 + - - +
101D HIS* 1.3 91.8 - - + +
103D LEU* 1.3 62.3 + - - +
105D GLU* 3.3 8.3 + - + +
106D GLU* 3.0 31.0 + - + +
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Residues in contact with LEU 103 (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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11D ALA* 4.0 28.9 - - + +
14D ILE* 4.0 26.7 - - + -
15D LEU* 3.7 29.2 - - + -
26D LEU* 5.4 0.9 - - + -
43D LEU* 4.3 18.2 - - + -
99D LEU 3.0 21.4 + - - +
100D TYR* 3.9 12.8 - - + +
101D HIS 3.3 0.2 - - - -
102D LEU* 1.3 75.6 - - - +
104D ALA* 1.3 59.9 + - - +
106D GLU* 3.2 5.2 + - + +
107D LYS 3.1 3.8 + - - -
108D LEU* 2.9 43.6 + - + +
109D CYS* 3.9 11.7 - - - -
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Residues in contact with ALA 104 (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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100D TYR 2.9 17.7 + - - +
101D HIS 3.9 3.6 - - - +
103D LEU* 1.3 76.5 - - - +
105D GLU* 1.3 59.0 + - - +
107D LYS* 2.9 22.2 + - - +
109D CYS* 3.4 27.4 - - - +
110D PRO 4.2 0.9 - - - +
111D ALA* 4.0 23.8 - - + -
114D ARG* 4.4 14.4 - - + +
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Residues in contact with GLU 105 (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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141B ARG* 2.8 39.6 + - - -
101D HIS* 3.1 52.3 + - + +
102D LEU* 3.6 9.4 - - + +
104D ALA* 1.3 71.4 - - - +
106D GLU* 1.3 64.7 + - + +
107D LYS* 3.0 24.0 + - - +
114D ARG* 4.5 9.0 + - - +
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Residues in contact with GLU 106 (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 LYS* 4.6 8.4 + - + +
25D TYR* 3.4 19.9 + - - -
26D LEU* 3.8 25.3 - - + +
29D LYS* 2.7 33.5 + - - +
30D LEU* 5.6 3.7 - - + +
43D LEU* 6.2 1.8 - - + -
102D LEU* 3.0 23.1 + - + +
103D LEU* 3.2 5.1 + - + +
104D ALA 3.2 0.2 - - - -
105D GLU* 1.3 78.5 - - + +
107D LYS* 1.3 72.4 + - - +
108D LEU* 3.2 25.8 + - + +
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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