Contacts of the strand formed by residues 173 - 182 (chain D) in PDB entry 2GJ6
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 PHE 173 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122D ASP* 6.0 0.4 - - - -
143D ASP* 3.5 28.0 - - + -
166D LEU 3.9 0.7 - - - +
167D ASP* 4.1 0.3 - - - +
168D MET* 3.2 46.6 + - + +
171D MET* 3.3 10.5 - - + +
172D ASP* 1.3 75.3 - - - +
174D LYS* 1.3 72.1 + - - +
175D SER* 3.5 24.4 + - - -
140E THR* 6.5 0.4 - - - -
142E LYS* 3.7 41.7 - - + -
197E ARG* 4.1 2.9 - - - -
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Residues in contact with LYS 174 (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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14D GLU* 3.0 32.2 + - - +
82D PRO* 3.5 19.8 - - + +
116D PRO* 4.0 29.2 - - + -
117D ASP 4.6 9.4 - - - +
118D ILE* 3.6 16.3 - - + +
165D VAL* 5.0 3.4 - - + -
166D LEU 3.5 6.7 - - - +
167D ASP* 3.5 36.2 + - + +
172D ASP* 3.7 10.4 + - - +
173D PHE* 1.3 88.7 - - - +
175D SER* 1.3 63.3 + - - +
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Residues in contact with SER 175 (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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116D PRO* 5.8 0.4 - - - +
118D ILE* 4.8 3.4 - - - -
142D THR* 4.5 0.2 - - - -
143D ASP* 3.3 28.7 - - - +
164D THR 3.8 0.7 - - - +
165D VAL* 3.6 2.9 - - - +
166D LEU* 3.1 53.7 + - - +
173D PHE* 3.5 9.3 - - - -
174D LYS* 1.3 77.5 - - - +
176D ASN* 1.3 69.9 + - - +
177D SER 3.8 0.3 + - - -
197E ARG* 3.3 15.7 + - - -
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Residues in contact with ASN 176 (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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116D PRO* 3.5 27.2 - - - +
118D ILE* 3.9 5.5 - - - +
142D THR* 3.2 4.7 + - - -
143D ASP* 2.9 29.0 + - - +
144D PHE* 3.5 43.9 + - + +
145D ASP 3.9 5.9 - - - +
146D SER* 3.4 21.0 + - - -
163D LYS* 4.2 13.5 - - + +
164D THR 3.4 4.6 + - - +
165D VAL* 3.6 17.4 - - - +
175D SER* 1.3 72.9 - - - +
177D SER* 1.3 58.9 + - - +
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Residues in contact with SER 177 (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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140D LEU* 4.0 15.3 - - - -
141D PHE 3.3 7.2 - - - -
142D THR* 3.6 14.1 - - - -
144D PHE* 3.9 3.6 - - - -
162D ASP 3.9 0.2 - - - +
163D LYS* 3.5 1.0 - - - -
164D THR* 2.9 39.9 + - - -
166D LEU* 4.2 12.4 - - - +
175D SER 4.9 1.3 - - - -
176D ASN* 1.3 77.5 - - - +
178D ALA* 1.3 63.5 + - - +
144E THR* 5.9 0.9 - - - -
173E SER* 4.7 0.7 + - - -
195E ARG* 3.3 26.2 + - - +
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Residues in contact with ALA 178 (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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139D CYS 3.9 0.2 - - - +
140D LEU* 3.6 3.8 - - - +
141D PHE* 2.9 38.8 + - + +
144D PHE* 4.6 2.5 - - + -
150D VAL* 4.3 23.3 - - + -
161D THR* 3.8 22.2 - - - +
162D ASP 4.1 4.5 - - - +
163D LYS* 4.3 4.5 - - - -
177D SER* 1.3 75.8 - - - +
179D VAL* 1.3 65.9 + - - +
193D PHE* 4.7 5.1 - - + -
195E ARG* 4.7 2.0 - - - +
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Residues in contact with VAL 179 (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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138D VAL* 3.9 34.3 - - + -
139D CYS 3.5 3.1 - - - +
140D LEU* 3.9 19.3 - - + -
159D TYR 3.8 0.9 - - - +
160D ILE* 3.8 1.5 - - - +
161D THR* 2.9 42.0 + - + +
178D ALA* 1.3 79.6 - - - +
180D ALA* 1.3 61.3 + - - +
181D TRP* 3.9 14.5 - - + -
193D PHE* 4.8 2.0 - - - -
146E VAL* 4.2 13.0 - - + -
148E LEU* 5.5 1.1 - - + -
193E SER* 4.3 10.8 - - - +
195E ARG* 3.6 25.4 - - - +
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Residues in contact with ALA 180 (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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138D VAL* 3.8 0.9 - - - -
139D CYS* 2.9 35.1 + - + +
158D VAL* 4.9 0.9 - - + -
159D TYR 3.4 4.7 - - - -
160D ILE* 4.0 22.0 - - + -
179D VAL* 1.3 74.7 - - - +
181D TRP* 1.3 63.1 + - - +
187D PHE* 4.5 5.9 - - + -
192D ALA* 4.4 13.7 - - + -
193D PHE* 3.7 27.3 - - + -
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Residues in contact with TRP 181 (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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136D LYS* 4.5 12.2 - - + +
137D SER 3.3 21.8 - - - +
138D VAL* 3.8 6.3 - - + -
158D VAL 3.8 0.5 - - - -
159D TYR* 2.9 69.1 + + + -
161D THR* 3.7 28.3 - - + -
179D VAL* 3.9 17.5 - - + -
180D ALA* 1.3 74.8 - - - +
182D SER* 1.3 69.2 + - - +
183D ASN* 5.8 0.9 - - - -
187D PHE* 4.1 9.0 - - - -
148E LEU* 3.7 39.9 - - + +
150E THR* 4.4 9.3 - - + +
179E LEU* 4.2 13.7 - - + -
181E GLU* 5.5 1.7 + - + -
191E ALA* 3.7 31.4 - - + -
193E SER* 4.6 2.7 - - - -
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Residues in contact with SER 182 (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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136D LYS* 3.4 17.5 - - - +
137D SER 4.5 3.4 + - - +
157D ASP* 2.6 36.4 + - - +
158D VAL* 3.9 2.5 + - - +
159D TYR* 4.5 0.7 - - - -
181D TRP* 1.3 82.7 - - - +
183D ASN* 1.3 66.3 + - - +
184D LYS 4.1 9.8 + - - +
187D PHE* 3.7 40.7 - - - +
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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
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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