Contacts of the strand formed by residues 177 - 183 (chain A) in PDB entry 3GUU
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 LYS 177 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A PRO* 6.1 6.3 - - + +
85A PRO 3.6 5.2 + - - +
86A LYS* 3.4 20.9 - - + +
87A ILE* 2.8 27.7 + - - +
175A ASP 3.2 2.3 + - - +
176A SER* 1.3 73.2 - - - +
178A VAL* 1.3 58.7 + - - +
205A ASN* 3.6 16.8 - - - +
207A VAL* 3.6 24.2 - - + -
384A ALA 5.3 0.9 + - - -
385A PHE* 3.1 48.1 + - + +
386A ASP 5.1 4.4 - - - -
387A GLY* 5.2 1.8 - - - +
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ILE* 3.3 18.8 - - + +
89A SER* 5.2 0.2 - - - -
163A ILE* 3.9 39.7 - - + -
167A LYS* 5.3 1.3 - - + -
176A SER 3.5 14.8 - - - +
177A LYS* 1.3 75.3 - - - +
179A ALA* 1.3 67.9 + - - +
180A LEU* 4.0 20.4 - - + -
204A LEU* 4.7 7.6 - - + -
205A ASN 3.0 20.0 + - - +
206A ILE* 3.3 15.0 - - + +
207A VAL* 2.9 30.0 + - - +
208A GLY 3.7 0.9 + - - -
385A PHE* 4.0 3.1 - - - -
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Residues in contact with ALA 179 (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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87A ILE 2.9 7.8 + - - +
88A PHE* 3.4 5.2 - - + -
89A SER* 2.8 32.4 + - - -
178A VAL* 1.3 75.6 - - - +
180A LEU* 1.3 59.3 + - - +
207A VAL* 4.8 2.0 - - + -
208A GLY* 3.2 18.2 - - - +
381A ILE* 3.8 24.2 - - + +
384A ALA* 5.4 0.4 - - + -
385A PHE* 3.6 26.8 - - + -
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Residues in contact with LEU 180 (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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89A SER* 3.4 9.6 - - - -
91A GLN* 3.7 13.0 - - - +
159A ILE* 3.9 15.5 - - + -
160A LEU* 5.3 0.9 - - + -
163A ILE* 4.1 9.2 - - + -
178A VAL* 4.0 9.2 - - + -
179A ALA* 1.3 80.5 - - - +
181A GLU* 1.3 64.3 + - - +
190A THR* 3.9 13.7 - - + +
193A ALA* 3.9 28.9 - - + -
194A THR* 4.7 5.8 - - + +
206A ILE* 3.7 42.4 - - + -
208A GLY 3.2 7.9 + - - +
209A ALA* 3.3 8.9 - - + -
210A SER 2.9 25.3 + - - -
381A ILE* 3.6 4.3 - - - +
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Residues in contact with GLU 181 (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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88A PHE* 3.7 26.0 - - + -
89A SER 2.9 7.5 + - - +
90A TYR* 3.2 34.8 - - - -
91A GLN* 2.9 27.6 + - - +
126A ILE* 3.6 20.7 - - - +
180A LEU* 1.3 76.2 - - - +
182A GLY* 1.3 69.1 + - - +
183A TYR* 5.6 1.0 - - - +
190A THR* 3.7 5.8 - - - -
210A SER* 3.1 17.5 - - - +
329A TRP* 3.5 16.3 - - - -
374A LEU* 5.8 1.4 - - - +
377A SER* 3.0 27.1 + - - +
378A LEU* 4.5 7.6 - - + +
381A ILE* 4.5 2.5 - - + -
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Residues in contact with GLY 182 (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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90A TYR* 4.6 1.6 - - - -
91A GLN 3.6 13.9 - - - -
181A GLU* 1.3 86.6 + - - +
183A TYR* 1.3 61.1 + - - +
186A GLY 4.0 1.6 - - - -
187A ALA* 3.8 6.1 - - - -
190A THR* 3.6 11.5 + - - -
210A SER 3.1 6.5 + - - +
211A HIS* 3.1 26.5 - - - +
212A GLY 3.2 2.1 + - - -
329A TRP* 4.2 3.1 - - - -
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Residues in contact with TYR 183 (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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90A TYR* 5.4 4.3 + - + +
91A GLN 4.2 2.0 + - - -
93A TYR* 3.6 16.7 - + + -
122A ASP* 5.3 2.0 - - - +
126A ILE* 6.4 1.8 - - + -
181A GLU* 5.6 1.1 - - - +
182A GLY* 1.3 74.1 - - - +
184A SER* 1.3 80.1 + - - +
186A GLY* 2.9 18.5 + - - -
187A ALA 3.4 4.2 - - - +
212A GLY 3.3 23.8 - - - -
213A GLY* 3.5 10.7 - - - -
329A TRP* 3.4 41.5 - + + -
330A HIS* 6.0 0.2 - - - -
331A ALA 5.2 1.0 + - - -
334A ASP* 4.5 1.0 + - - -
366A HIS* 2.6 57.8 + + - -
369A ALA* 3.8 8.3 - - - +
370A GLU* 3.5 44.5 + - + +
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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