Contacts of the strand formed by residues 129 - 139 (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 THR 129 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124D GLN* 3.0 42.8 + - + +
125D LEU* 3.7 5.7 - - - +
127D SER* 3.2 24.4 - - - +
128D GLY* 1.3 79.6 - - - +
130D ALA* 1.3 65.4 + - - +
180D THR* 5.0 4.0 + - - -
181D LEU 4.0 7.1 + - - -
182D SER* 4.7 1.3 - - - +
183D LYS* 4.3 1.1 - - - +
126E PHE* 5.2 1.8 - - + -
147E LYS* 3.5 26.8 + - + +
148E ASP* 5.1 3.4 - - - +
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Residues in contact with ALA 130 (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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120D PRO* 3.9 18.2 - - + -
124D GLN* 3.8 5.2 - - - -
125D LEU* 4.1 7.2 - - + -
129D THR* 1.3 79.4 + - - +
131D SER* 1.3 62.2 + - - +
132D VAL* 4.3 1.3 - - - -
179D LEU 3.8 0.5 - - - +
180D THR* 3.7 1.9 + - - -
181D LEU* 2.7 45.5 + - + +
182D SER 4.3 3.8 - - - +
183D LYS 4.4 0.2 - - - +
186D TYR* 3.9 29.2 - - + -
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Residues in contact with SER 131 (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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118D PHE 4.3 0.2 - - - +
119D PRO 4.3 1.4 - - - +
120D PRO* 3.6 19.4 - - - +
124D GLN* 2.8 33.8 + - - +
130D ALA* 1.3 75.4 - - - +
132D VAL* 1.3 63.4 + - - +
133D VAL* 4.0 5.6 + - - +
178D THR* 3.7 24.0 - - - -
179D LEU 3.3 5.6 - - - -
180D THR* 4.5 7.2 - - - -
128E LEU* 5.4 3.1 - - - +
145E LEU* 3.2 20.6 - - - +
147E LYS* 4.3 5.5 - - - +
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Residues in contact with VAL 132 (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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117D ILE* 4.1 3.1 - - + -
118D PHE 3.4 12.8 - - - +
120D PRO* 3.8 22.4 - - + -
130D ALA 5.5 0.2 - - - -
131D SER* 1.3 73.1 - - - +
133D VAL* 1.3 60.2 + - - +
148D TRP* 3.7 23.7 - - + -
177D SER 3.6 1.4 - - - +
178D THR* 3.4 3.8 - - - -
179D LEU* 2.9 51.5 + - + +
181D LEU* 4.9 3.1 - - + -
186D TYR* 4.3 9.9 - - + -
192D TYR* 4.4 4.7 - - + -
209D PHE* 3.3 35.4 - - + -
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Residues in contact with VAL 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D ILE* 3.4 5.2 - - - +
118D PHE* 2.8 53.2 + - + -
131D SER 4.6 3.1 - - - +
132D VAL* 1.3 74.6 - - - +
134D CYS* 1.3 67.7 + - - +
135D LEU* 4.5 4.7 - - + +
148D TRP* 4.2 2.9 - - - -
176D SER* 4.7 12.6 - - - -
177D SER 3.6 2.5 - - - +
178D THR* 3.5 24.5 - - + +
128E LEU* 3.9 31.9 - - + -
145E LEU* 4.0 17.0 - - + -
183E SER* 4.3 8.7 - - - +
185E VAL* 5.6 2.7 - - + -
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Residues in contact with CYS 134 (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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115D VAL* 4.0 7.2 - - - -
116D PHE 3.6 3.1 - - - -
117D ILE* 4.7 0.4 - - - +
133D VAL* 1.3 72.9 - - - +
135D LEU* 1.3 59.3 + - - +
136D LEU* 3.8 21.6 - - - +
146D VAL* 3.8 6.5 - - - -
148D TRP* 3.1 19.9 - - + -
175D LEU 3.7 1.9 - - - +
176D SER* 3.4 2.4 - - - -
177D SER* 2.8 41.8 + - - +
194D CYS* 2.0 47.8 - - + -
196D VAL* 4.4 0.4 - - - -
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Residues in contact with LEU 135 (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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114D SER 3.3 4.3 - - - +
115D VAL* 3.3 2.8 - - - +
116D PHE* 2.8 64.6 + - + +
118D PHE* 4.1 17.3 - - + -
133D VAL* 3.9 5.8 - - + -
134D CYS* 1.3 72.3 - - - +
136D LEU* 1.3 66.4 + - - +
137D ASN* 4.1 18.2 - - + +
174D SER* 4.9 0.4 - - - -
175D LEU 3.5 5.4 - - - +
176D SER* 4.6 1.8 - - - +
141E ALA* 4.0 16.6 - - + -
170E PHE* 3.7 31.0 - - + -
185E VAL* 3.7 26.7 - - + -
187E THR* 5.6 0.4 - - + -
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Residues in contact with LEU 136 (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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113D PRO* 3.7 16.2 - - + -
114D SER 3.4 5.2 - - - -
115D VAL* 4.5 2.9 - - + -
134D CYS* 3.8 20.0 - - - +
135D LEU* 1.3 75.8 - - - +
137D ASN* 1.3 59.6 + - - +
139D PHE* 3.6 11.3 - - + -
144D ALA* 4.1 18.6 - - + -
146D VAL* 4.5 7.9 - - + +
174D SER* 3.4 4.3 - - - -
175D LEU* 2.8 63.7 + - + +
196D VAL* 3.6 47.3 - - + -
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Residues in contact with ASN 137 (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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113D PRO* 3.7 0.2 - - - +
114D SER* 2.7 47.2 + - - +
116D PHE* 4.0 15.0 - - + -
135D LEU* 4.1 15.8 - - + +
136D LEU* 1.3 74.8 - - - +
138D ASN* 1.3 85.2 + - - +
139D PHE* 3.8 1.3 - - - -
174D SER* 3.0 20.3 + - - -
168E HIS* 3.2 21.0 + - - -
185E VAL* 5.4 0.7 - - - +
187E THR* 3.4 31.4 + - - +
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Residues in contact with ASN 138 (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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111D ALA* 4.3 7.8 - - - +
112D ALA 3.6 11.3 - - - +
114D SER* 5.2 0.8 + - - +
137D ASN* 1.3 94.4 + - - +
139D PHE* 1.3 59.2 + - - +
167D ASP* 4.3 2.3 - - - +
170D ASP* 3.8 16.5 + - - +
172D THR* 3.2 26.9 + - + +
173D TYR 3.4 5.7 + - - -
174D SER* 3.2 9.9 + - - -
168E HIS* 3.5 23.5 + - - -
187E THR* 4.9 4.2 + - - -
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Residues in contact with PHE 139 (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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111D ALA* 3.3 15.9 - - - +
113D PRO* 3.6 34.3 - - + -
136D LEU* 3.6 13.9 - - + -
138D ASN* 1.3 74.7 - - - +
140D TYR* 1.3 62.6 + - - +
141D PRO 3.2 20.0 - - - -
142D ARG* 3.2 33.7 - - - -
144D ALA* 4.4 9.0 - - + -
163D VAL* 4.4 2.7 - - + -
172D THR* 3.5 4.8 - - - -
173D TYR* 2.8 60.8 + - + +
174D SER 4.3 0.2 - - - -
175D LEU* 3.5 41.7 - - + -
198D HIS* 3.7 8.3 - + - +
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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