Contacts of the strand formed by residues 86 - 91 (chain B) 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 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ALA* 4.0 14.2 + - + +
83B SER 3.6 8.1 + - - +
84B PRO* 3.1 38.3 + - - +
85B PRO* 1.3 74.8 - - - +
87B ILE* 1.3 62.3 + - - +
88B PHE 4.1 0.2 - - - -
134B GLY 5.4 0.8 + - - -
135B TYR* 3.6 36.7 - - + -
136B TYR* 3.0 31.2 + - - -
177B LYS* 3.5 14.4 - - + +
385B PHE* 3.6 49.1 + - + -
386B ASP* 4.4 9.6 - - - +
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Residues in contact with ILE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LYS* 1.3 74.8 - - - +
88B PHE* 1.3 60.4 + - - +
89B SER 4.7 0.2 - - - +
136B TYR* 3.4 3.8 - - + +
138B VAL* 4.1 16.2 - - + -
163B ILE* 4.4 17.3 - - + +
166B LEU* 3.8 25.4 - - + -
167B LYS* 3.2 40.6 - - + -
172B LEU* 3.9 22.2 - - + -
176B SER* 3.9 13.7 - - - -
177B LYS 2.8 12.4 + - - +
178B VAL* 3.4 13.6 - - + +
179B ALA 3.0 26.3 + - - +
385B PHE* 3.3 4.3 - - - -
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Residues in contact with PHE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LYS 4.1 0.4 - - - -
87B ILE* 1.3 72.5 - - - +
89B SER* 1.3 59.5 + - - +
90B TYR* 3.8 16.6 - - + -
126B ILE* 3.5 33.2 - - + -
127B ILE* 4.3 2.9 - - + -
129B TRP* 4.5 5.8 - + - -
130B ALA* 3.6 24.5 - - + -
135B TYR* 4.1 18.8 - - + -
136B TYR 2.8 13.1 + - - +
137B VAL* 3.3 14.3 - - + -
138B VAL 3.1 23.8 + - - +
179B ALA 3.5 6.3 - - - -
181B GLU* 3.7 30.7 - - + -
378B LEU* 4.4 4.5 - - + -
381B ILE* 3.8 35.0 - - + -
385B PHE* 4.1 3.1 - + + -
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Residues in contact with SER 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 4.0 1.7 + - - -
88B PHE* 1.3 72.9 - - - +
90B TYR* 1.3 59.9 + - - +
91B GLN* 2.7 26.1 + - - -
138B VAL* 3.2 24.7 + - - +
139B SER* 5.3 0.5 - - - -
140B SER* 5.4 2.3 + - - -
159B ILE* 3.7 11.8 + - - +
163B ILE* 3.9 20.3 - - - +
178B VAL* 5.3 0.4 - - - -
179B ALA 2.9 14.5 + - - -
180B LEU* 3.3 6.9 - - - -
181B GLU* 3.0 25.6 + - - +
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Residues in contact with TYR 90 (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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88B PHE* 3.8 10.7 + + + -
89B SER* 1.3 70.6 + - - +
91B GLN* 1.3 74.4 + - - +
92B VAL* 3.8 15.4 - - + -
93B TYR* 4.4 14.2 - - - -
107B TYR* 3.5 16.2 - - - -
122B ASP* 4.6 1.9 + - - -
123B THR* 3.0 45.4 + - + -
126B ILE* 3.7 27.0 - - + +
127B ILE* 3.4 26.5 - - + -
137B VAL* 4.8 0.2 - - + -
138B VAL 2.9 10.8 + - - +
139B SER* 2.7 34.7 + - - +
140B SER 4.5 0.7 + - - -
181B GLU* 3.1 33.0 - - - -
182B GLY* 4.5 3.1 - - - -
183B TYR* 5.4 2.1 + - - +
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Residues in contact with GLN 91 (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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89B SER* 2.7 42.9 + - - -
90B TYR* 1.3 90.3 + - - +
92B VAL* 1.3 60.7 + - - +
93B TYR* 4.0 0.7 + - - -
139B SER* 4.7 0.2 - - - -
140B SER* 5.2 3.3 + - - +
142B HIS* 4.5 7.4 - - + +
159B ILE* 3.5 38.7 - - + +
180B LEU* 3.8 11.1 - - - +
181B GLU 2.8 17.8 + - - +
182B GLY* 3.6 11.6 - - - -
183B TYR 4.3 1.2 + - - -
186B GLY* 3.3 29.8 - - - +
189B ALA* 4.0 8.1 - - + -
190B THR* 3.0 23.7 + - - +
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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
------------------------------------------------------------
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