Contacts of the strand formed by residues 173 - 182 (chain D) in PDB entry 6IAP
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 TYR 173 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D SER* 4.8 1.0 + - - -
103D LYS* 5.1 0.7 - - - -
105D GLU* 2.7 47.7 + - - +
138D ASN* 3.4 4.1 - - - -
139D PHE* 2.8 59.6 + - + +
140D TYR* 3.5 28.3 - + - -
142D ARG* 3.6 47.0 - - + +
163D VAL* 4.2 6.3 - - + -
164D THR* 3.5 21.8 - - - -
165D GLU* 5.1 0.2 - - - -
166D GLN* 3.7 30.1 + - + -
172D THR* 1.3 74.7 - - - +
174D SER* 1.3 61.0 + - - +
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Residues in contact with SER 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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135D LEU* 4.9 0.9 - - - -
136D LEU 3.4 10.3 - - - -
137D ASN* 3.0 23.9 + - - -
138D ASN* 3.2 12.5 + - - -
139D PHE* 3.7 0.9 - - - -
163D VAL* 3.3 3.7 - - - +
164D THR* 2.8 37.8 + - - -
173D TYR* 1.3 70.8 + - - +
175D LEU* 1.3 61.4 + - - +
168E HIS* 3.4 22.2 + - - -
170E PHE* 3.2 17.6 - - - -
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Residues in contact with LEU 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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134D CYS 3.7 1.4 - - - +
135D LEU* 3.5 3.6 - - - +
136D LEU* 2.8 58.3 + - + +
139D PHE* 3.5 20.6 - - + -
142D ARG* 5.0 5.8 - - + +
144D ALA* 5.0 7.9 - - + +
146D VAL* 3.7 29.2 - - + -
161D GLU* 3.7 20.9 - - + +
162D SER 3.5 9.0 - - - +
163D VAL* 3.9 22.7 - - + -
174D SER* 1.3 75.4 - - - +
176D SER* 1.3 69.6 + - - +
177D SER 4.8 0.2 - - - +
170E PHE* 3.6 3.8 - - - -
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Residues in contact with SER 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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133D VAL* 4.7 13.7 - - - -
134D CYS 3.4 5.2 - - - -
135D LEU* 4.6 2.5 - - - +
160D GLN 4.0 0.9 + - - +
161D GLU* 3.3 5.0 - - - +
162D SER* 2.9 44.1 + - - -
175D LEU* 1.3 77.0 - - - +
177D SER* 1.3 60.1 + - - +
178D THR* 4.5 7.5 + - - -
170E PHE* 3.4 27.9 - - - +
183E SER* 5.3 7.2 + - - -
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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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133D VAL* 3.6 0.7 - - - -
134D CYS* 2.8 47.1 + - - -
146D VAL* 3.7 25.5 + - - +
148D TRP* 3.2 30.9 + - - -
159D SER* 4.5 4.0 + - - -
160D GLN 3.7 5.4 + - - -
161D GLU* 3.7 14.2 + - - +
175D LEU* 4.9 0.9 - - - -
176D SER* 1.3 74.9 - - - +
178D THR* 1.3 60.0 + - - +
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Residues in contact with THR 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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131D SER* 3.7 28.0 - - - +
132D VAL 3.4 5.6 - - - +
133D VAL* 3.5 22.5 - - + +
158D ASN 4.2 0.2 - - - +
159D SER* 3.3 5.0 - - - -
160D GLN* 3.1 36.0 + - - +
176D SER* 4.1 8.4 + - - -
177D SER* 1.3 71.9 + - - +
179D LEU* 1.3 62.7 + - - +
180D THR* 3.7 10.0 + - + +
145E LEU* 4.6 7.0 - - + +
173E VAL* 6.3 2.9 - - - -
181E SER* 6.0 1.3 - - - +
183E SER* 4.6 5.9 + - - -
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Residues in contact with LEU 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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130D ALA 3.8 1.0 - - - +
131D SER* 3.3 4.6 - - - -
132D VAL* 2.9 40.8 + - + +
148D TRP* 3.8 50.0 - - + +
149D LYS 6.3 1.1 - - - -
150D VAL* 5.7 3.1 - - + -
155D GLN* 4.6 5.2 - - + -
158D ASN* 3.3 39.0 - - - +
159D SER* 3.9 6.3 - - - -
177D SER 4.0 1.4 + - - -
178D THR* 1.3 69.8 - - - +
180D THR* 1.3 57.8 + - - +
181D LEU* 3.3 25.2 + - + +
192D TYR* 4.1 20.0 - - + -
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Residues in contact with THR 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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129D THR* 5.0 5.0 + - - -
130D ALA 3.7 6.0 + - - -
131D SER* 4.5 9.6 - - - +
158D ASN* 3.1 36.5 + - - +
159D SER* 5.0 0.9 - - - -
160D GLN* 5.3 9.6 - - + -
178D THR* 4.2 11.4 - - + +
179D LEU* 1.3 72.1 - - - +
181D LEU* 1.3 66.3 + - - +
147E LYS* 5.2 8.3 + - - -
175E GLN* 5.4 12.8 + - + +
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Residues in contact with LEU 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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129D THR* 4.0 4.3 + - - -
130D ALA* 2.7 34.1 + - - +
132D VAL* 4.9 5.4 - - + -
150D VAL* 5.4 5.8 - - + -
155D GLN* 5.9 1.3 - - - +
158D ASN* 4.9 7.6 - - + +
179D LEU* 3.3 46.7 - - + +
180D THR* 1.3 76.6 + - - +
182D SER* 1.3 65.3 + - - +
185D ASP* 3.6 35.2 - - + +
186D TYR* 4.2 10.3 - - + +
189D HIS* 5.6 2.5 - - + -
192D TYR* 4.4 15.7 - - + +
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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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128D GLY 4.1 7.9 - - - -
129D THR* 4.7 1.6 - - - +
130D ALA* 4.3 2.0 - - - +
181D LEU* 1.3 77.4 - - - +
183D LYS* 1.4 54.4 + - - +
184D ALA* 3.7 9.6 + - - +
185D ASP* 3.0 37.1 + - - -
186D TYR* 2.8 32.1 + - - +
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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