Contacts of the strand formed by residues 137 - 142 (chain N) in PDB entry 2AK4
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 SER 137 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127N GLN* 3.1 27.9 + - - +
128N LEU 5.4 0.2 + - - -
130N ASP* 3.8 14.0 + - - -
135N ASP 4.4 0.2 + - - -
136N LYS* 1.3 74.6 - - - +
138N VAL* 1.3 62.9 + - - +
139N CYS* 5.5 0.5 - - - -
181N TRP* 3.3 13.0 - - - +
182N SER 3.5 13.6 + - - -
187N PHE* 3.2 32.0 + - - -
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Residues in contact with VAL 138 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127N GLN* 3.6 6.8 - - - +
128N LEU* 3.0 41.8 + - + +
137N SER* 1.3 76.8 + - - +
139N CYS* 1.3 69.7 - - - +
140N LEU 4.6 0.2 - - - +
179N VAL* 3.7 23.1 - - + -
180N ALA 3.5 1.6 - - - -
181N TRP* 3.8 17.0 - - + -
131P PHE* 3.6 48.2 - - + -
147P VAL* 4.2 15.3 - - + -
149P LEU* 4.1 9.4 - - + -
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Residues in contact with CYS 139 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125N VAL* 4.3 0.9 - - + -
126N TYR 3.3 4.3 - - - +
127N GLN* 5.3 1.8 - - - -
137N SER* 5.5 0.2 - - - -
138N VAL* 1.3 75.9 - - - +
140N LEU* 1.3 60.5 + - - +
179N VAL* 3.6 3.5 - - - -
180N ALA 2.7 41.2 + - - +
187N PHE* 3.6 28.0 - - + -
189N CYS* 2.0 55.9 - - + -
192N ALA* 4.2 1.3 - - + -
193N PHE* 3.7 20.9 - - + -
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Residues in contact with LEU 140 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124N ALA 3.4 2.3 - - - +
125N VAL* 3.2 5.2 - - - -
126N TYR* 2.8 45.3 + - + +
128N LEU* 3.7 26.9 - - + -
138N VAL* 4.2 0.6 - - + -
139N CYS* 1.3 73.1 - - - +
141N PHE* 1.3 59.0 + - - +
142N THR* 3.9 22.5 + - + -
177N SER* 4.0 24.5 - - - +
178N ALA 3.7 2.7 - - - +
179N VAL* 4.0 21.8 - - + -
137P GLU* 4.7 2.2 - - - +
145P THR* 3.7 33.9 - - + +
147P VAL* 4.1 13.2 - - + -
196P ARG* 4.5 1.8 - - + -
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Residues in contact with PHE 141 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123N PRO* 4.3 16.4 - - + -
124N ALA 3.4 17.7 - - - -
125N VAL* 3.7 11.9 - - + -
140N LEU* 1.3 70.5 - - - +
142N THR* 1.3 61.1 + - - +
144N PHE* 3.3 45.3 - + + -
148N THR* 4.0 15.7 - - + -
149N ASN 6.0 0.2 - - - -
150N VAL* 4.2 14.6 - - + -
177N SER* 3.1 3.8 - - - -
178N ALA* 2.8 37.4 + - + +
193N PHE* 3.5 39.0 - + + -
196N SER* 6.0 1.1 - - - -
198N ILE* 3.8 26.0 - - + -
199N PRO* 4.2 5.6 - - + -
202N THR* 4.4 10.1 - - + -
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Residues in contact with THR 142 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123N PRO* 3.6 0.7 - - - +
124N ALA 3.1 25.0 + - - +
126N TYR* 3.7 34.5 - - + -
140N LEU* 4.0 16.2 - - + -
141N PHE* 1.3 75.8 - - - +
143N ASP* 1.3 91.7 + - - +
144N PHE* 3.2 7.3 + - - -
175N SER* 4.4 1.4 + - - -
176N ASN 3.0 13.5 + - - -
177N SER* 3.8 11.6 - - - -
137P GLU* 5.0 0.7 - - - +
145P THR* 5.3 1.0 + - - -
198P ARG* 3.7 14.2 + - - +
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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