Contacts of the strand formed by residues 195 - 205 (chain A) in PDB entry 4GUP
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 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A GLU* 3.4 7.1 - - - +
191A THR* 3.4 20.2 + - - +
192A PHE* 2.5 59.2 + - + +
194A GLY* 1.3 76.2 - - - +
196A THR* 1.3 68.6 + - - +
245A GLU* 4.1 30.5 - - + +
246A LEU 4.5 7.2 - - - +
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Residues in contact with THR 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ARG* 5.4 10.1 - - + -
189A LYS 3.3 9.0 - - - +
190A GLU* 3.7 25.1 - - + +
191A THR* 4.6 0.2 - - - -
194A GLY 4.2 3.2 + - - +
195A VAL* 1.3 78.5 - - - +
197A ALA* 1.3 59.9 + - - +
245A GLU* 4.2 0.3 - - - -
246A LEU* 3.1 50.0 + - - +
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Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ARG* 3.5 3.4 - - - -
189A LYS* 2.8 34.0 + - - +
191A THR* 3.7 33.2 - - + +
195A VAL 4.4 0.2 + - - -
196A THR* 1.3 74.5 - - - +
198A LEU* 1.3 65.8 - - - +
199A PHE* 3.7 9.9 + - + -
243A SER* 5.1 1.6 - - - -
244A ILE 3.2 17.3 - - - +
245A GLU* 4.6 4.0 - - + -
246A LEU* 4.3 0.7 - - - +
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Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A VAL* 4.6 4.7 - - + -
187A ASN 4.5 0.7 - - - -
188A ARG* 3.8 34.1 - - + +
197A ALA* 1.3 71.3 - - - +
199A PHE* 1.3 59.9 + - - +
214A TRP* 3.6 18.9 + - + -
243A SER* 3.3 7.3 - - - -
244A ILE* 3.0 42.2 + - + -
246A LEU* 3.7 29.6 - - + +
254A TYR* 4.0 29.8 - - + -
269A VAL* 3.9 32.5 - - + -
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Residues in contact with PHE 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ARG 3.7 1.0 - - - +
186A VAL* 3.2 8.3 - - - +
187A ASN* 2.9 57.0 + - - +
189A LYS* 3.7 28.3 - - + -
191A THR* 4.1 22.2 - - + -
197A ALA* 4.0 4.3 - - + -
198A LEU* 1.3 77.8 - - - +
200A CYS* 1.3 60.6 + - - +
201A LYS* 3.8 13.6 + - + -
214A TRP* 4.1 0.4 - - - -
241A TRP* 3.8 38.8 - + + -
242A ALA 3.9 1.8 - - - -
243A SER* 3.6 27.1 - - - -
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Residues in contact with CYS 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A VAL* 3.6 20.2 - - - -
185A ARG 3.7 4.0 - - - -
186A VAL* 4.1 3.6 - - + -
199A PHE* 1.3 71.2 - - - +
201A LYS* 1.3 63.1 + - - +
212A MET* 3.7 22.4 - - - -
214A TRP* 3.8 17.1 - - + +
241A TRP* 3.1 26.5 - - - +
242A ALA* 3.0 13.4 + - + +
256A CYS* 2.8 39.3 - - - -
258A VAL* 4.4 2.0 - - - -
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Residues in contact with LYS 201 (chain A).
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 3.5 3.6 - - - +
184A VAL* 3.3 3.9 - - - -
185A ARG* 2.8 61.7 + - - +
187A ASN* 3.7 27.1 - - - +
199A PHE* 4.3 16.2 - - + +
200A CYS* 1.3 77.7 - - - +
202A ALA* 1.3 58.8 + - - +
203A HIS* 5.4 0.7 - - + -
239A GLN* 6.3 1.3 - - - +
240A ALA 3.8 5.2 - - - +
241A TRP* 4.5 22.1 - - + -
97B ARG 6.0 1.2 + - - -
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Residues in contact with ALA 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A PRO* 4.3 6.5 - - + -
183A LEU 3.6 4.9 - - - -
184A VAL* 3.7 23.8 - - + +
200A CYS 4.2 1.2 + - - -
201A LYS* 1.3 72.0 - - - +
203A HIS* 1.4 60.5 + - - +
205A PHE* 4.0 10.8 - - + -
210A ILE* 4.5 1.3 - - + -
212A MET* 3.2 29.1 - - + +
239A GLN* 3.4 2.9 - - - +
240A ALA 2.9 33.7 + - - +
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Residues in contact with HIS 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A PRO* 3.5 1.0 - - - +
183A LEU* 2.8 75.8 + - + +
185A ARG* 4.2 8.9 + - - -
201A LYS 5.4 0.2 - - - -
202A ALA* 1.4 75.1 - - - +
204A GLY* 1.3 66.6 + - - +
205A PHE* 3.3 5.5 + - - -
233A SER* 5.8 0.9 - - - +
238A TYR 3.5 7.0 - - - -
239A GLN* 4.0 16.4 - - + +
12B ARG 5.2 4.5 - - - +
13B HIS* 5.2 6.1 - - + -
14B PRO* 3.6 37.6 - - + +
183C LEU* 3.9 20.8 - - + +
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Residues in contact with GLY 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLU* 3.3 21.8 - - - +
181A PRO 3.6 8.5 - - - +
183A LEU* 5.4 6.4 - - - +
203A HIS* 1.3 81.2 - - - +
205A PHE* 1.3 59.2 + - - +
233A SER* 5.2 1.0 + - - -
237A THR* 3.4 23.4 + - - +
238A TYR 3.0 7.7 + - - -
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Residues in contact with PHE 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLU* 3.2 12.8 - - - +
181A PRO 4.1 0.4 - - - -
182A PRO* 3.7 31.0 - - + -
202A ALA* 3.7 12.1 - - + -
203A HIS* 3.9 6.1 - - - -
204A GLY* 1.3 78.4 - - - +
206A TYR* 1.4 60.0 + - - +
207A PRO 3.7 13.7 - - - -
208A PRO* 3.9 13.0 - - + -
210A ILE* 3.7 37.0 - - + -
230A ILE* 4.0 4.5 - - + -
237A THR* 3.4 6.6 - - - -
238A TYR* 2.9 62.0 + - + -
239A GLN* 3.7 17.9 - - - -
240A ALA* 4.0 2.0 - - + -
260A HIS* 3.8 13.0 - + - +
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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