Contacts of the strand formed by residues 150 - 160 (chain B) in PDB entry 4I9X
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 HIS 150 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ILE* 3.8 4.7 - - - -
40B GLU* 3.3 40.8 + - + +
42B MSE 3.7 22.4 - - + -
74B TRP* 3.7 3.0 - - + -
146B ARG* 3.4 2.9 - - - -
147B ASN* 2.7 45.1 + - - +
149B SER* 1.3 103.2 + - - +
151B GLY* 1.3 58.6 + - - +
115C ARG* 4.8 5.6 - - - -
1F NAG 3.5 39.8 - - - +
2F NAG 3.5 20.0 + - + -
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Residues in contact with GLY 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 3.3 13.8 - - - +
40B GLU 3.2 5.9 + - - -
41B LYS* 3.7 3.3 - - - -
42B MSE 2.8 37.2 + - - +
74B TRP* 4.6 0.2 - - - -
144B VAL* 3.6 13.5 - - - -
145B LEU 3.1 9.9 - - - -
146B ARG* 4.1 1.8 - - - -
150B HIS* 1.3 74.3 - - - +
152B LEU* 1.3 56.8 + - - -
153B ILE* 3.7 3.1 - - - +
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LEU* 4.6 13.7 - - + -
42B MSE 3.5 18.4 - - + +
43B TRP 3.6 9.0 - - - +
44B ALA* 3.4 28.5 - - - +
74B TRP* 3.9 34.1 - - + +
144B VAL* 3.4 0.4 - - - -
145B LEU* 2.8 39.6 + - + +
151B GLY* 1.3 69.9 - - - -
153B ILE* 1.3 64.8 + - - +
154B MSE 3.3 21.8 + - - +
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Residues in contact with ILE 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ILE* 4.6 6.1 - - + -
41B LYS* 3.9 23.3 - - + -
42B MSE 2.7 22.4 + - - +
43B TRP* 3.6 25.4 - - + +
44B ALA 3.1 20.9 + - - -
47B TYR* 3.4 32.8 - - + -
80B ARG* 4.2 15.7 - - - +
142B GLU* 3.4 30.3 - - + +
143B CYS 3.8 3.6 - - - +
144B VAL* 4.0 18.8 - - + +
151B GLY 4.3 2.9 - - - +
152B LEU* 1.3 72.7 - - - +
154B MSE 1.3 61.4 + - - +
155B GLN 4.3 0.4 - - - +
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Residues in contact with MSE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A TYR* 5.7 5.6 - - + -
183A LEU* 4.2 28.5 - - + -
44B ALA* 4.0 12.4 - - + +
46B ASN* 4.6 2.7 - - - +
47B TYR* 3.8 13.5 - - - -
50B THR* 3.6 12.3 + - - +
68B THR 5.8 1.6 - - - +
69B VAL* 4.4 16.4 - - + -
143B CYS* 2.8 26.8 + - + +
145B LEU* 4.0 28.7 - - + +
152B LEU* 3.6 32.8 - - - +
153B ILE* 1.3 73.1 - - - +
155B GLN* 1.3 64.0 + - + +
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Residues in contact with GLN 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B TYR* 3.8 4.6 - - - -
50B THR* 2.8 40.1 + - - +
51B SER* 3.7 8.5 - - - +
52B PRO* 4.6 0.8 - - - +
66B PRO 4.2 3.5 - - - +
67B CYS* 5.1 1.9 - - - -
68B THR 5.1 4.2 + - - +
141B TYR 4.0 0.2 - - - +
142B GLU* 3.1 6.2 - - - +
143B CYS* 2.9 39.5 + - - -
153B ILE 3.6 1.8 - - - -
154B MSE 1.3 85.9 - - + +
156B ARG* 1.3 62.6 + - - +
157B PHE* 3.3 37.4 - - + -
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Residues in contact with ARG 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B TYR* 3.2 39.5 + - + +
48B GLU* 4.3 11.9 + - - -
51B SER* 2.9 30.5 + - - +
52B PRO* 3.4 16.4 + - - +
82B ARG* 4.6 3.1 - - - +
140B MSE 4.4 10.3 - - + -
141B TYR 3.4 7.4 - - - +
142B GLU* 3.7 15.0 - - + -
155B GLN* 1.3 73.6 - - - +
157B PHE* 1.3 73.7 + - - +
158B VAL* 3.8 20.0 - - + +
237B VAL* 3.6 28.7 - - - +
241B TYR* 2.9 28.7 + - - -
147C GLU 4.8 1.0 + - - -
148C ASP* 3.0 31.1 + - - +
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Residues in contact with PHE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A THR* 5.7 1.3 - - + -
70A MSE 3.8 31.0 - - + -
123A LEU* 5.4 6.3 - - + -
52B PRO* 4.0 25.4 - - + -
55B VAL* 6.3 0.2 - - + -
65B ILE* 3.7 34.1 - - + -
66B PRO* 3.6 33.9 - - + -
139B GLY 3.7 1.0 - - - +
140B MSE 3.5 1.7 - - - -
141B TYR* 2.7 46.6 + - - +
143B CYS* 3.9 11.9 - - - -
155B GLN* 3.3 37.5 - - + -
156B ARG* 1.3 74.4 - - - +
158B VAL* 1.3 62.7 + - - +
159B ILE* 3.9 7.1 + - + -
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B PRO 5.0 6.0 + - - +
53B ALA 4.9 0.6 + - - +
54B PRO* 3.4 26.3 - - + +
55B VAL* 3.0 30.0 + - - +
139B GLY 3.5 9.2 - - - +
140B MSE 4.2 13.5 - - + -
156B ARG* 3.8 30.7 - - - +
157B PHE* 1.3 76.3 - - - +
159B ILE* 1.3 61.1 + - - +
160B LEU* 3.8 23.1 - - + -
234B CYS* 4.7 3.8 - - + -
237B VAL* 4.0 15.7 - - + -
238B ILE* 4.8 6.1 - - + -
241B TYR* 5.4 0.9 - - + -
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Residues in contact with ILE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A LEU* 3.7 29.4 - - + -
55B VAL* 3.8 15.3 - - + -
57B VAL* 4.2 16.8 - - + -
63B VAL* 4.9 2.7 - - + -
65B ILE* 3.9 14.6 - - + -
131B PHE* 4.7 7.2 - - + -
133B VAL* 4.1 30.7 - - + -
138B ALA* 3.3 6.8 - - - +
139B GLY 2.9 32.4 + - - +
141B TYR* 3.7 27.8 - - + -
157B PHE* 4.5 8.7 - - + +
158B VAL* 1.3 73.2 - - - +
160B LEU* 1.3 65.2 + - - +
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Residues in contact with LEU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B PRO* 3.7 27.8 - - + -
55B VAL 2.9 17.0 + - - +
56B LEU* 3.5 12.4 - - + -
57B VAL* 2.9 30.8 + - - +
84B CYS* 4.3 13.9 - - - -
138B ALA* 4.3 3.6 - - - -
158B VAL* 3.8 18.8 - - + -
159B ILE* 1.3 78.3 - - - +
161B THR* 1.3 64.1 + - - +
162B GLN 4.5 7.0 - - - +
163B LEU* 4.0 27.1 - - + -
187B ILE* 5.1 4.7 - - + -
238B ILE* 3.6 29.4 - - + -
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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