Contacts of the strand formed by residues 202 - 212 (chain B) in PDB entry 4IF8
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 MET 202 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LEU* 3.8 31.6 - - + -
139B PHE 3.2 13.0 - - - +
140B ILE* 3.8 26.0 - - + -
167B PHE* 4.1 0.9 - - - -
200B THR* 3.4 5.7 - - - +
201B VAL* 1.3 82.3 - - - +
203B LEU* 1.3 64.6 + - - +
338B LEU* 3.7 26.9 - - + -
341B ILE* 4.0 11.2 - - + -
347B LEU* 3.8 16.8 - - + -
348B LYS 3.6 25.3 + - - +
349B VAL* 3.8 13.0 - - + -
350B GLY 2.8 26.2 + - - -
351B GLU 3.4 3.5 + - - -
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Residues in contact with LEU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B THR 3.7 0.9 - - - +
138B LEU* 3.7 5.2 - - - -
139B PHE* 2.9 48.4 + - + +
167B PHE* 3.9 15.0 - - + -
177B ILE* 3.9 21.3 - - + -
193B ILE* 4.0 28.5 - - + -
196B ILE* 4.4 9.2 - - + -
200B THR* 4.5 0.4 - - + -
202B MET* 1.3 76.3 - - - +
204B LEU* 1.3 74.0 + - - +
205B ALA* 4.3 3.6 - - + +
349B VAL* 4.9 0.4 - - - -
351B GLU* 3.1 44.4 - - + +
352B ALA 4.9 0.2 - - - +
353B VAL* 5.7 0.2 - - + -
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Residues in contact with LEU 204 (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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82B ALA* 3.8 22.9 - - + +
83B PHE* 4.0 16.6 - - + -
85B MET* 3.9 26.7 - - + -
86B LEU* 3.8 24.5 - - + -
136B ASN* 4.5 8.5 - - - +
137B THR 3.6 13.2 - - - +
138B LEU* 4.1 13.0 - - + -
203B LEU* 1.3 74.5 - - - +
205B ALA* 1.3 75.3 + - - +
206B ASN* 4.8 1.6 - - + +
319B LEU* 4.8 2.2 - - + -
349B VAL* 4.3 6.7 - - + +
351B GLU 2.7 10.1 + - - +
352B ALA* 3.2 12.8 - - + -
353B VAL* 2.9 30.0 + - - +
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Residues in contact with ALA 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLY 3.7 1.6 - - - +
136B ASN* 3.5 3.6 + - - -
137B THR* 2.9 39.9 + - - +
139B PHE* 4.0 19.1 - - + -
181B ILE* 4.0 10.7 - - + +
192B LEU* 3.8 27.4 - - + -
203B LEU* 4.1 3.7 + - + -
204B LEU* 1.3 75.3 - - - +
206B ASN* 1.3 58.8 + - - +
207B TYR* 4.3 2.4 - - + -
353B VAL* 3.8 6.3 - - + -
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Residues in contact with ASN 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B SER* 2.7 47.6 + - - +
79B ILE* 3.9 2.1 + - - -
81B THR* 3.7 0.4 + - - -
82B ALA* 3.8 13.6 - - + +
134B ILE* 4.3 0.4 - - - +
135B GLY 3.3 5.2 + - - -
136B ASN* 2.7 32.5 + - - +
192B LEU* 5.7 1.6 - - - +
204B LEU* 5.0 1.8 - - + -
205B ALA* 1.3 73.2 - - - +
207B TYR* 1.3 59.3 + - - +
319B LEU* 4.7 5.6 - - + -
353B VAL* 2.9 14.6 + - - +
354B HIS* 2.7 30.6 + - - +
355B LYS* 2.9 23.0 + - - +
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Residues in contact with TYR 207 (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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78B SER* 3.7 6.1 + - - -
133B SER* 4.3 23.3 - - - -
134B ILE* 3.4 3.8 - - - -
135B GLY* 2.8 57.5 + - - +
137B THR* 5.8 0.2 - - - -
181B ILE* 4.7 17.9 - - + -
184B LYS* 3.6 34.0 + - + +
185B THR* 3.4 28.0 - - + +
189B ILE* 3.6 31.2 - - + -
192B LEU* 6.0 4.3 - - + -
205B ALA* 5.6 1.8 - - + -
206B ASN* 1.3 77.2 - - - +
208B ILE* 1.3 68.2 + - - +
209B PHE* 4.3 7.4 - - + -
355B LYS* 3.2 13.5 - - + +
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Residues in contact with ILE 208 (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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75B SER* 3.4 39.5 - - - +
77B LEU* 5.2 1.1 - - + -
78B SER* 3.7 10.3 - - - +
132B LEU* 4.1 13.0 - - + -
133B SER 3.2 11.9 - - - +
134B ILE* 4.0 20.4 - - + -
189B ILE* 5.7 1.0 - - - +
207B TYR* 1.3 78.8 - - - +
209B PHE* 1.3 67.6 + - - +
354B HIS* 4.1 0.7 - - + -
355B LYS 3.0 8.4 + - - +
356B ALA* 3.8 10.3 - - + -
357B GLU* 2.9 29.8 + - - +
403B LEU* 4.0 14.4 - - + +
404B PHE* 3.6 31.2 - - + -
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Residues in contact with PHE 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LYS* 3.9 30.5 - - + -
132B LEU* 3.3 8.1 - - - +
133B SER* 3.0 50.9 + - - +
188B LYS* 3.6 46.9 - - + +
189B ILE* 6.0 2.5 - - + -
207B TYR* 4.3 10.9 - - + -
208B ILE* 1.3 74.1 - - - +
210B PHE* 1.3 64.5 + - - +
211B ARG* 3.3 46.9 - - - -
357B GLU* 3.6 24.0 - - + -
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Residues in contact with PHE 210 (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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130B LEU* 3.5 21.8 - - + -
131B LYS 3.4 3.8 - - - -
132B LEU* 3.8 21.1 - - + -
209B PHE* 1.3 76.9 - - - +
211B ARG* 1.3 76.0 + - - +
212B ALA* 3.6 26.5 - - + -
264B TYR* 3.9 23.6 - + - -
268B ILE* 4.1 11.0 - - + -
357B GLU 2.9 8.4 + - - +
358B LEU* 3.5 23.6 - - + -
359B LYS 3.3 18.8 + - - -
394B ILE* 4.0 14.4 - - + -
403B LEU* 3.8 19.7 - - + -
404B PHE* 3.4 28.5 - + + -
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Residues in contact with ARG 211 (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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128B GLN 5.5 0.7 - - - +
129B ASP 4.8 0.2 - - - -
130B LEU* 3.7 0.7 - - - -
131B LYS* 2.8 55.9 + - + +
209B PHE* 3.3 43.1 - - + -
210B PHE* 1.3 94.2 + - - +
212B ALA* 1.3 58.8 - - - +
312B HIS* 3.4 21.6 + - - -
357B GLU* 2.8 34.2 + - - +
359B LYS* 3.4 46.6 - - + +
363B ARG* 4.8 13.2 - - - +
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLN 5.5 0.7 - - - -
129B ASP 3.5 14.1 - - - +
130B LEU* 3.8 10.3 - - + -
210B PHE* 3.6 23.3 - - + -
211B ARG* 1.3 74.8 - - - +
213B ARG* 1.3 61.8 + - - +
214B TRP* 4.0 1.9 + - - -
264B TYR* 3.6 36.8 - - + -
266B LYS* 6.2 0.4 - - + -
268B ILE* 5.5 0.4 - - + -
359B LYS 4.9 5.7 + - - +
363B ARG* 4.4 6.9 - - - +
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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