Contacts of the strand formed by residues 108 - 122 (chain B) in PDB entry 2IZW
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 TYR 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B ASP 6.0 0.4 - - - -
63B THR* 3.2 35.4 + - + +
104B GLN* 3.3 28.0 - - + +
105B GLY 2.9 16.4 + - - +
106B SER 3.5 0.6 + - - -
107B ARG* 1.3 95.3 - - + +
109B SER* 1.3 59.4 + - - +
110B LYS 4.2 2.2 - - - +
184B SER* 3.0 9.1 - - - -
225B LEU* 3.6 42.4 - - + -
226B THR* 3.8 25.1 - - - +
227B ASP 3.5 2.2 - - - -
228B PRO* 3.7 29.1 - - + +
229B VAL* 3.7 5.2 - - - -
234B ASN* 2.9 8.8 + - - -
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Residues in contact with SER 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A MET 4.8 1.2 + - - -
137A LEU* 4.9 1.4 - - - +
138A TYR* 3.4 44.3 + - - -
108B TYR* 1.3 71.6 - - - +
110B LYS* 1.3 57.4 + - - +
183B LEU* 3.7 5.8 - - - +
184B SER* 2.6 36.5 + - - +
227B ASP* 2.7 19.0 + - - -
229B VAL* 2.7 22.8 - - - +
234B ASN* 4.5 3.3 - - - +
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A TYR* 3.4 39.2 - - - -
172A TYR* 4.5 3.2 + - - -
176A HIS* 3.0 31.3 + - + +
177A ALA* 3.7 5.3 - - - +
178A SER* 3.0 31.2 + - - +
182A TYR* 4.1 5.5 + - - -
198A PRO 4.1 4.6 + - - -
108B TYR* 4.2 3.5 - - - +
109B SER* 1.3 80.3 - - - +
111B TYR* 1.3 67.8 + - - +
181B TRP* 4.2 7.6 - - + -
182B TYR 3.1 10.3 - - - +
183B LEU* 3.6 14.6 - - + -
184B SER* 4.4 0.6 - - - +
225B LEU* 3.7 3.5 - - - +
226B THR* 3.0 37.0 + - + +
227B ASP* 3.7 15.5 - - - +
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Residues in contact with TYR 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE* 3.5 10.7 + + - -
91B ASN* 3.7 3.5 + - - -
92B VAL* 3.4 41.3 - - + -
110B LYS* 1.3 80.4 - - - +
112B ARG* 1.3 71.7 + - - +
113B VAL* 4.5 13.2 - - + -
181B TRP* 3.4 8.0 - - - -
182B TYR* 2.6 57.8 + - + +
183B LEU 3.7 14.8 - - - -
184B SER* 4.2 0.9 - - - -
196B GLN 2.5 29.8 + - - -
198B PRO* 3.1 24.3 - - + +
223B VAL* 4.7 5.2 - - + -
224B GLU 3.1 14.8 - - - +
225B LEU* 4.0 15.5 - - + -
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Residues in contact with ARG 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE* 3.8 8.1 - - - +
111B TYR* 1.3 81.6 - - - +
113B VAL* 1.3 65.8 + - - +
114B ARG* 3.5 24.2 - - - +
180B PRO 3.5 21.6 + - - +
181B TRP* 3.3 48.8 - - + +
182B TYR* 4.9 6.5 - - + +
223B VAL* 3.4 3.8 - - - +
224B GLU* 2.5 80.3 + - + +
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE* 3.9 29.8 - - + -
111B TYR* 4.5 7.9 - - + -
112B ARG* 1.3 79.4 - - - +
114B ARG* 1.3 65.2 + - - +
115B TYR 3.6 23.1 - - - +
116B ALA* 4.1 9.4 - - + -
172B TYR* 3.5 40.6 - - + -
174B PRO* 3.9 7.1 - - - +
182B TYR* 5.7 2.0 - - - -
198B PRO* 4.1 19.7 - - + +
199B PHE* 4.4 1.8 - - + -
222B LEU 4.1 4.5 - - - +
223B VAL* 4.2 6.5 - - + +
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Residues in contact with ARG 114 (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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112B ARG* 3.5 28.8 + - - +
113B VAL* 1.3 74.7 - - - +
115B TYR* 1.3 70.8 + - + +
174B PRO* 3.4 16.8 - - - +
222B LEU* 2.9 39.4 + - + -
224B GLU* 3.1 31.6 + - + +
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Residues in contact with TYR 115 (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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66B LYS* 3.5 32.2 - - + +
113B VAL* 3.4 6.2 - - - +
114B ARG* 1.3 89.3 - - + +
116B ALA* 1.3 65.2 + - - +
117B HIS* 3.4 38.1 - + + +
172B TYR* 5.0 2.9 - - - +
174B PRO* 4.9 4.5 - - + -
220B GLU* 3.9 15.2 + - - +
221B TYR* 3.5 18.6 + - - +
222B LEU* 3.0 59.6 + - + +
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Residues in contact with ALA 116 (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 PHE* 4.4 2.9 - - + -
113B VAL* 4.1 13.9 - - + -
115B TYR* 1.3 78.2 - - - +
117B HIS* 1.3 65.2 + - - +
118B PHE* 3.7 26.3 - - + -
171B SER* 3.3 3.6 - - - -
172B TYR* 3.0 37.9 + - + +
199B PHE* 4.2 4.5 - - + -
220B GLU 3.5 6.7 - - - +
221B TYR* 4.1 10.1 - - + -
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Residues in contact with HIS 117 (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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115B TYR* 3.4 33.7 - + + -
116B ALA* 1.3 75.6 - - - +
118B PHE* 1.3 62.5 + - - +
119B THR* 4.7 3.2 - - + +
169B ARG* 3.3 55.3 + - + +
170B LEU 3.3 3.1 - - - -
171B SER* 2.8 28.2 + - - +
218B MET 3.8 0.5 - - - +
219B ALA* 3.3 3.6 - - - -
220B GLU* 2.9 54.0 + - + +
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Residues in contact with PHE 118 (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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71B LEU* 4.0 17.5 - - + -
90B PHE* 3.8 14.6 - + - -
116B ALA* 3.7 26.2 - - + -
117B HIS* 1.3 73.2 - - - +
119B THR* 1.3 64.0 + - - +
134B MET* 3.9 20.2 - - + +
136B MET* 4.9 5.2 - - - -
166B THR* 4.9 0.7 - - - +
169B ARG* 3.5 5.5 - - - +
170B LEU* 2.7 54.5 + - + +
171B SER* 5.0 0.2 - - - -
172B TYR 4.9 0.2 - - - -
199B PHE* 3.5 34.1 - + - -
201B ILE* 3.5 25.1 - - + -
217B ILE* 4.9 0.2 - - + -
218B MET 3.2 8.1 - - - +
219B ALA* 3.5 31.0 - - + -
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Residues in contact with THR 119 (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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117B HIS* 4.7 4.9 - - + +
118B PHE* 1.3 79.3 - - - +
120B TRP* 1.3 68.2 + - - +
134B MET* 4.3 7.8 - - - +
165B PRO* 5.9 0.3 - - - +
166B THR* 3.5 24.9 + - - -
169B ARG* 4.8 8.5 - - + -
217B ILE* 3.5 4.7 - - - +
218B MET* 2.7 55.2 + - + +
219B ALA 4.9 0.2 - - - +
220B GLU* 5.8 2.9 - - + +
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Residues in contact with TRP 120 (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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74B VAL* 3.8 30.3 - - + -
119B THR* 1.3 76.8 + - - +
121B GLU* 1.3 59.9 + - - +
122B PRO* 3.4 19.1 - - + +
132B VAL* 3.9 31.8 - - + +
134B MET* 4.5 9.8 - - - -
161B PRO 4.7 1.6 - - - -
162B ILE* 2.8 45.0 + - + +
164B SER 3.5 22.7 - - - -
165B PRO* 3.6 2.9 - - - +
166B THR* 2.7 36.9 + - - +
214B LEU* 3.7 7.2 - - + -
215B GLY* 3.3 38.1 - - - -
216B ARG 3.0 24.0 - - - -
217B ILE* 4.0 9.9 - - + +
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Residues in contact with GLU 121 (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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119B THR 3.8 0.4 + - - -
120B TRP* 1.3 75.3 - - - +
122B PRO* 1.3 75.7 - - - +
123B ILE* 3.8 7.6 - - + +
165B PRO* 5.3 3.6 - - - +
215B GLY* 3.1 3.5 - - - -
216B ARG* 2.8 64.7 + - + +
218B MET* 3.7 24.7 - - + -
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Residues in contact with PRO 122 (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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120B TRP* 3.4 18.3 - - + +
121B GLU* 1.3 100.6 - - - +
123B ILE* 1.3 62.5 + - - +
124B VAL 3.7 4.9 - - - +
162B ILE 3.1 26.7 - - - +
163B TRP* 3.2 26.9 - - - +
165B PRO* 3.7 25.1 - - + -
214B LEU 3.8 5.2 - - - +
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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