Contacts of the strand formed by residues 195 - 203 (chain B) in PDB entry 3U4S
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 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B ILE* 4.3 4.5 - - + -
35B GLU* 2.6 32.0 + - - -
194B LEU* 1.3 74.7 - - - +
196B SER* 1.3 61.7 + - - +
269B ILE* 4.4 2.0 - - + -
270B THR 3.2 14.4 - - - +
271B PHE* 3.6 12.8 - + - -
272B PRO* 3.4 33.4 - - + -
290B ASN* 2.7 18.2 + - - -
291B PHE* 3.1 62.5 + + + +
292B ALA* 3.9 7.2 - - - -
293B THR* 2.8 45.0 + - + +
295B ARG* 3.4 10.2 + - - +
296B TRP* 3.9 6.1 - - + -
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Residues in contact with SER 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B GLU* 3.5 12.3 - - - -
195B TYR* 1.3 72.9 - - - +
197B ILE* 1.3 60.5 + - - +
198B ASN* 5.6 0.2 - - - +
268B MET 4.7 0.2 - - - -
269B ILE* 3.4 4.5 - - - -
270B THR* 2.8 49.0 + - - +
288B SER* 4.6 0.2 - - - -
289B THR 3.4 8.7 - - - -
290B ASN* 3.3 18.6 - - - -
291B PHE* 3.5 9.5 - - - -
503B 08P 2.8 26.8 + - - -
9D M3L 4.2 4.0 - - - -
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Residues in contact with ILE 197 (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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27B PHE* 3.6 29.6 - - + -
148B TRP* 3.7 8.1 - - + -
150B ILE* 4.0 16.4 - - + -
153B LEU* 3.8 17.0 - - + -
196B SER* 1.3 74.1 - - - +
198B ASN* 1.3 59.6 + - - +
267B PHE* 3.7 33.0 - - + -
268B MET 3.5 3.6 - - - +
269B ILE* 3.8 12.6 - - + -
287B GLU 4.5 0.4 - - - -
288B SER* 2.8 35.4 + - - -
289B THR* 3.0 31.5 + - + +
291B PHE* 3.8 6.7 - - + -
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Residues in contact with ASN 198 (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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177B TYR* 5.4 0.3 - - - -
196B SER* 5.6 0.4 - - - +
197B ILE* 1.3 75.7 - - - +
199B TYR* 1.3 62.0 + - - +
206B LYS* 3.9 1.5 - - - +
208B TRP* 3.8 21.0 - - + -
262B GLN* 3.1 28.0 + - - +
267B PHE* 3.3 3.7 - - - -
268B MET* 2.7 42.2 + - + +
270B THR* 6.2 0.2 - - + -
286B ALA* 3.7 22.9 - - - +
287B GLU 3.5 5.6 - - - -
288B SER* 4.0 6.3 - - - -
503B 08P 3.3 41.8 + - - +
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Residues in contact with TYR 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PRO* 5.3 0.2 - - - +
53B TRP* 3.6 24.9 - + - -
55B PRO* 3.6 24.6 - - + +
59B TYR* 4.3 0.9 + - - -
141B TYR* 4.2 4.3 - + - -
150B ILE* 3.8 14.5 - - + +
198B ASN* 1.3 76.4 - - - +
200B LEU* 1.3 63.7 + - - +
201B HIS* 3.5 50.3 + + - -
265B GLY* 3.6 31.5 + - - -
266B GLU 3.7 6.3 - - - -
267B PHE* 3.4 42.0 - + + -
286B ALA* 3.3 2.1 - - - -
287B GLU* 2.9 32.4 + - + +
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Residues in contact with LEU 200 (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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199B TYR* 1.3 73.8 - - - +
201B HIS* 1.3 61.1 + - - +
202B PHE 3.6 7.7 + - - +
203B GLY 4.7 0.4 - - - +
204B GLU 3.6 20.0 - - - +
205B PRO* 4.0 0.4 - - + -
206B LYS* 4.0 13.5 - - - +
262B GLN* 3.4 32.4 - - + +
263B GLU 3.8 9.0 - - - +
264B ALA* 3.6 23.3 - - + +
265B GLY* 2.8 32.2 + - - -
266B GLU 3.1 8.9 + - - -
284B ASN* 4.0 19.5 - - + +
285B CYS 3.6 17.7 - - - +
286B ALA* 3.9 15.5 - - + -
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Residues in contact with HIS 201 (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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55B PRO* 4.3 4.0 - - + -
59B TYR* 2.7 47.9 + + + +
140B LEU* 3.7 28.1 - - + +
141B TYR* 4.0 14.6 - + - -
199B TYR* 3.5 26.9 + + - -
200B LEU* 1.3 74.0 - - - +
202B PHE* 1.3 72.4 + - + +
264B ALA* 4.5 1.4 - - - +
265B GLY* 4.4 5.2 + - - -
285B CYS* 2.9 18.3 + - - +
287B GLU* 2.8 52.3 + - + +
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Residues in contact with PHE 202 (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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59B TYR* 3.5 50.5 - + + -
62B ILE* 4.0 21.3 - - + -
94B VAL* 5.6 0.9 - - + -
140B LEU* 4.5 0.2 - - + -
178B PHE* 4.7 1.6 - + - -
200B LEU* 3.5 4.4 - - - +
201B HIS* 1.3 82.1 - - + +
203B GLY* 1.3 68.0 + - - +
264B ALA* 3.9 12.3 - - - -
283B PHE* 3.8 33.9 - + - -
284B ASN* 3.4 4.7 - - - +
285B CYS* 3.1 56.0 + - + +
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Residues in contact with GLY 203 (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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200B LEU* 4.7 0.4 - - - +
202B PHE* 1.3 85.0 - - - +
204B GLU* 1.3 73.7 + - - +
205B PRO* 4.1 0.7 - - - +
264B ALA* 3.6 18.4 + - - +
283B PHE* 3.4 14.6 - - - -
284B ASN* 3.9 1.6 - - - -
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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