Contacts of the strand formed by residues 160 - 167 (chain D) in PDB entry 1GGE
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 THR 160 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137D TYR* 3.4 1.7 - - - -
138D PHE* 2.7 53.9 + - - +
152D PHE* 3.4 25.1 + - + +
158D LYS* 4.5 5.5 + - - +
159D ILE* 1.3 76.1 + - - +
161D PRO* 1.3 77.4 - - - +
189D PHE* 3.9 18.6 - - + -
190D TYR 3.6 26.5 - - - +
191D THR* 4.1 9.2 - - + +
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Residues in contact with PRO 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D ASN* 3.5 25.4 - - + +
63D GLU* 3.8 37.7 - - + +
64D LYS* 3.7 16.8 - - + +
136D GLY 3.5 7.9 - - - +
137D TYR* 4.3 2.2 - - + -
159D ILE* 3.7 10.1 - - + +
160D THR* 1.3 90.5 - - - +
162D VAL* 1.3 58.5 + - - +
190D TYR* 3.1 47.4 + - + +
437D THR* 5.4 0.2 - - - +
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Residues in contact with VAL 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ASN* 4.9 1.2 + - - -
64D LYS* 6.0 0.5 - - - +
135D HIS* 3.5 6.4 + - - +
136D GLY* 2.8 51.8 + - - +
137D TYR 3.8 2.0 - - - +
138D PHE* 4.0 7.6 - - + -
160D THR 3.9 7.2 - - - +
161D PRO* 1.3 79.9 - - - +
163D PHE* 1.3 62.1 + - - +
164D VAL* 4.1 2.7 - - + -
187D THR* 3.8 13.7 - - + -
188D LYS 3.1 9.0 - - - +
189D PHE* 3.7 31.6 - - + -
190D TYR* 3.9 5.9 - - - -
373D MET* 3.6 22.7 - - + -
375D LEU* 4.0 6.5 - - + -
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Residues in contact with PHE 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ALA* 3.4 27.6 - - + -
134D ALA* 3.5 19.3 - - - -
135D HIS* 3.6 40.4 - + - +
162D VAL* 1.3 74.0 - - - +
164D VAL* 1.3 60.2 + - - +
165D ARG* 5.3 0.2 - - + -
188D LYS* 2.9 32.3 + - + -
190D TYR* 3.6 21.3 - - + +
379D PRO* 4.6 4.7 - - + -
385D GLU* 3.3 38.4 - - + -
386D ASN* 4.1 2.9 - - + -
389D ALA* 3.8 11.4 - - + -
391D PHE* 3.5 21.0 - + - -
433D ILE* 3.8 15.3 - - + -
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Residues in contact with VAL 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D SER 4.0 0.3 - - - +
133D ALA* 3.0 6.8 - - - +
134D ALA 2.9 36.6 + - - +
162D VAL* 4.1 2.5 - - + -
163D PHE* 1.3 75.8 - - - +
165D ARG* 1.3 63.7 + - - +
166D PHE* 3.5 39.5 - - + -
185D PHE* 3.9 9.6 - - + -
186D ALA 3.1 9.2 - - - +
187D THR* 3.6 20.9 - - + +
373D MET* 3.7 24.5 - - + -
375D LEU* 3.7 18.4 - - + -
391D PHE* 4.5 0.9 - - - -
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Residues in contact with ARG 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D ARG* 3.3 32.8 - - - +
128D HIS 2.9 21.4 + - - -
129D ALA 3.0 27.1 + - - -
131D GLY* 3.2 16.4 + - - +
132D SER 3.5 10.3 - - - +
133D ALA* 3.9 4.7 - - + -
164D VAL* 1.3 75.0 - - - +
166D PHE* 1.3 69.0 + - - +
167D SER* 3.8 10.1 + - - -
184D GLY 4.1 0.9 - - - +
185D PHE* 3.8 1.0 + - - -
186D ALA* 2.8 33.2 + - - +
382D PHE* 5.9 0.8 - - - -
386D ASN* 2.9 29.7 + - - +
387D GLU* 4.8 1.8 + - - -
389D ALA* 5.2 0.4 - - - -
391D PHE* 3.6 18.0 - - + -
760D HDD 2.8 44.4 + - - +
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Residues in contact with PHE 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D GLY* 3.0 3.8 - - - -
132D SER 2.8 40.3 + - - +
134D ALA 6.0 0.4 - - - -
164D VAL* 3.5 23.6 - - + -
165D ARG* 1.3 73.6 - - - +
167D SER* 1.3 62.6 + - - +
184D GLY 3.2 4.3 - - - +
185D PHE* 3.8 36.1 - + - -
266D TYR* 3.5 44.9 + + + -
269D MET* 3.7 19.3 - - + -
322D LEU* 3.9 16.6 - - + -
334D TYR* 3.3 28.5 - + - -
375D LEU* 3.8 19.1 - - + -
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Residues in contact with SER 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D HIS* 2.8 28.3 + - - +
130D ARG 3.0 15.5 - - - -
131D GLY* 3.8 0.9 - - - -
165D ARG* 3.8 18.8 + - - -
166D PHE* 1.3 78.1 - - - +
168D THR* 1.3 68.0 + - - +
183D ARG* 3.0 13.5 - - - +
184D GLY* 2.7 34.4 + - - -
266D TYR* 4.1 6.4 + - - -
760D HDD 4.3 4.3 + - - +
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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