Contacts of the strand formed by residues 143 - 154 (chain B) in PDB entry 3IXK
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 143 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131B ASP 3.6 0.3 - - - +
132B LEU* 3.2 8.4 - - - -
133B VAL* 2.8 35.6 + - + +
141B VAL* 4.7 1.8 - - + -
142B THR* 1.3 82.0 - - - +
144B ARG* 1.3 67.2 + - - +
145B ALA* 3.8 4.4 + - + -
184B PHE* 3.8 31.6 - - + -
187B SER* 4.6 8.1 - - - -
188B LEU* 3.8 31.4 - - + -
191B GLN* 3.4 17.0 - - + +
192B THR* 3.8 17.9 - - + -
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Residues in contact with ARG 144 (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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107B THR* 2.9 49.1 + - - +
109B ARG* 3.4 44.3 - - - +
130B THR* 3.0 33.9 + - + +
131B ASP* 3.5 13.2 - - - +
132B LEU* 3.8 24.2 - - + +
143B VAL* 1.3 73.0 - - - +
145B ALA* 1.3 62.1 + - - +
187B SER* 3.8 3.1 + - - -
191B GLN* 2.7 42.0 + - - +
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Residues in contact with ALA 145 (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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86B PHE* 5.0 0.4 - - + -
130B THR* 3.3 6.8 - - - -
131B ASP 3.0 27.9 + - - +
133B VAL* 4.5 9.4 - - + -
143B VAL* 3.8 5.6 + - + -
144B ARG* 1.3 76.2 - - - +
146B ASN* 1.3 70.7 + - - +
147B ILE* 3.4 2.4 + - - +
184B PHE* 3.9 30.7 - - + -
187B SER* 4.2 15.5 - - - +
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Residues in contact with ASN 146 (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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86B PHE* 3.6 26.4 + - - +
111B LEU* 3.8 13.2 - - - +
128B LEU* 5.5 1.8 - - + -
129B GLY 3.7 3.4 - - - +
130B THR* 3.6 18.3 - - - +
145B ALA* 1.3 75.4 - - - +
147B ILE* 1.3 58.7 + - - +
181B LEU* 3.5 28.8 - - + +
182B GLU* 2.8 51.7 + - - +
184B PHE* 5.8 1.3 + - - +
187B SER* 4.8 1.2 + - - -
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Residues in contact with ILE 147 (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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68B VAL* 4.1 19.3 - - + -
86B PHE* 3.9 21.3 - - + +
88B VAL* 3.5 31.9 - - + +
100B TYR* 3.8 24.9 - - + +
108B TYR* 6.4 0.4 - - + -
127B GLU 3.7 0.7 - - - +
128B LEU* 3.5 5.5 - - - +
129B GLY* 2.7 40.4 + - - +
130B THR 4.6 0.2 - - - -
131B ASP* 3.5 32.8 - - + +
133B VAL* 4.2 5.8 - - + -
145B ALA 3.9 5.6 - - - +
146B ASN* 1.3 77.9 - - - +
148B ALA* 1.3 66.6 + - - +
149B ALA* 4.4 0.4 - - - +
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Residues in contact with ALA 148 (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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85B ASN* 5.2 4.9 - - - +
86B PHE 3.1 15.4 + - - +
87B ALA* 3.2 1.4 - - + +
88B VAL 2.9 27.9 + - - -
115B VAL* 4.3 4.5 - - + -
124B TRP* 3.5 34.5 - - + -
127B GLU 3.6 4.7 - - - -
128B LEU* 4.2 16.8 - - + -
147B ILE* 1.3 77.6 - - - +
149B ALA* 1.3 58.9 + - - +
150B ILE 3.5 1.8 + - - -
181B LEU* 6.1 0.2 - - + -
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Residues in contact with ALA 149 (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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88B VAL* 3.7 6.1 - - - -
90B ALA* 3.5 19.1 - - + -
100B TYR* 4.7 6.5 - - + -
102B ARG* 3.8 31.2 - - - +
126B GLY* 3.1 2.2 - - - -
127B GLU 2.8 36.8 + - - +
147B ILE* 3.9 3.3 - - + -
148B ALA* 1.3 68.7 - - - +
150B ILE* 1.3 66.9 + - - +
151B THR* 3.2 5.9 + - - +
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Residues in contact with ILE 150 (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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87B ALA* 3.7 27.8 - - + +
88B VAL* 2.8 29.6 + - - +
89B GLY* 4.0 3.3 - - - +
90B ALA* 3.1 23.6 + - - +
91B ALA* 3.7 4.0 + - - +
124B TRP* 3.5 42.4 - - + -
125B GLU 3.5 10.8 - - - +
126B GLY* 4.0 0.7 - - - -
149B ALA* 1.3 69.2 - - - +
151B THR* 1.3 60.5 + - - +
152B GLU 3.9 13.2 - - - +
153B SER* 4.2 1.1 - - - -
156B PHE* 4.0 14.4 - - + -
157B PHE* 3.9 24.2 - - + -
164B GLU 5.3 0.2 - - - +
165B GLY* 5.4 0.4 - - - -
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Residues in contact with THR 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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90B ALA* 5.2 0.7 - - + -
91B ALA* 4.1 22.6 - - + +
92B PRO 5.7 0.3 - - - +
102B ARG* 4.2 19.7 - - - +
125B GLU* 2.8 13.4 + - - +
126B GLY* 3.6 9.2 - - - -
127B GLU* 4.2 18.8 + - - +
149B ALA 3.2 8.6 + - - +
150B ILE* 1.3 77.9 - - - +
152B GLU* 1.3 70.2 + - - +
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Residues in contact with GLU 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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46A SER* 2.8 30.0 + - - +
47A PHE* 3.3 23.2 + - - +
48A VAL* 3.7 12.0 + - + -
124B TRP* 3.6 1.4 - - - +
125B GLU* 2.8 58.8 + - + +
150B ILE* 3.9 2.0 - - - +
151B THR* 1.3 88.8 + - - +
153B SER* 1.3 64.6 + - - +
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Residues in contact with SER 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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48A VAL* 3.6 10.0 - - - +
49A GLU* 5.5 2.4 - - - +
93B HIS* 3.7 20.2 + - - -
123B LYS 3.5 11.7 - - - -
124B TRP* 3.8 10.3 - - - -
150B ILE* 4.2 1.1 - - - -
152B GLU* 1.3 79.8 - - - +
154B ASP* 1.3 61.5 + - - +
155B LYS 4.2 1.1 + - - -
156B PHE* 4.3 7.1 + - - +
157B PHE* 3.5 34.9 + - - -
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Residues in contact with ASP 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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48A VAL* 4.2 4.0 - - + +
49A GLU* 3.9 30.0 - - + +
137A HIS* 5.5 5.4 + - - -
122B GLY* 3.6 1.7 - - - -
123B LYS* 2.9 61.7 + - + +
153B SER* 1.3 74.1 - - - +
155B LYS* 1.3 98.3 + - - +
156B PHE 3.1 2.1 + - - -
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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