Contacts of the strand formed by residues 140 - 145 (chain K) in PDB entry 3STJ
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 140 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13J PRO* 3.1 37.8 + - + -
14J SER* 3.6 16.4 - - - -
15J LEU* 3.8 26.0 - - + -
156J SER* 5.1 3.6 - - - -
135K LEU* 6.2 0.2 - - - +
138K GLY 4.5 0.2 - - - -
139K ASP* 1.3 76.6 - - - +
141K ALA* 1.3 60.0 + - - +
156K SER* 5.7 3.8 - - - +
157K GLY 3.6 7.6 - - - +
158K ILE* 3.7 24.2 - - + -
193K ASN* 3.9 19.1 - - - +
194K LEU* 3.8 34.3 + - + +
199K ILE* 4.8 2.9 - - - +
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Residues in contact with ALA 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139K ASP 3.8 0.2 + - - -
140K PHE* 1.3 74.7 - - - +
142K VAL* 1.3 64.8 + - - +
156K SER* 3.6 3.1 + - - -
157K GLY 2.9 34.8 + - - +
158K ILE 4.5 1.1 - - - -
159K VAL* 4.5 9.9 - - + -
178K THR* 4.2 13.2 - - - +
180K ALA* 4.5 1.4 - - - +
191K LEU* 3.8 22.4 - - + -
192K LEU 3.2 9.0 - - - +
199K ILE* 4.1 13.0 - - + -
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Residues in contact with VAL 142 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K LEU* 3.7 26.9 - - + -
18K MET* 4.1 18.4 - - + -
19K LEU* 4.1 24.2 - - + -
140K PHE* 6.4 0.2 - - + -
141K ALA* 1.3 76.7 - - - +
143K ALA* 1.3 67.8 + - - +
144K VAL* 4.3 3.8 - - + -
154K ALA* 4.3 10.8 - - + -
155K THR 3.3 13.9 - - - +
156K SER* 4.4 3.1 - - - +
190K ALA 3.5 3.3 - - - +
191K LEU* 3.6 3.1 - - - -
192K LEU* 2.7 46.8 + - + +
193K ASN 5.0 0.2 - - - +
194K LEU* 4.8 9.0 - - + -
158L ILE* 4.8 2.9 - - + -
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Residues in contact with ALA 143 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141K ALA 4.3 0.2 - - - -
142K VAL* 1.3 72.3 - - - +
144K VAL* 1.3 61.7 + - - +
153K THR 3.6 1.2 - - - +
154K ALA* 3.2 5.4 - - - -
155K THR* 2.7 54.8 + - - +
180K ALA* 4.0 15.0 - - + +
181K SER 4.5 0.4 - - - +
182K ILE* 4.1 13.0 - - + -
186K ASN* 4.5 4.4 - - - +
190K ALA 3.3 4.5 - - - -
191K LEU* 4.3 5.6 - - + -
202K ASN* 3.7 14.8 - - - +
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Residues in contact with VAL 144 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K LEU* 4.6 0.4 - - + -
23K LEU* 3.7 25.1 - - + -
26K VAL* 3.8 24.8 - - + +
142K VAL* 4.3 9.9 - - + -
143K ALA* 1.3 80.4 - - - +
145K GLY* 1.3 60.8 + - - +
152K GLN* 3.6 26.0 - - + -
153K THR 3.3 10.1 - - - +
154K ALA* 4.4 3.1 - - + -
186K ASN* 3.9 3.7 - - - +
189K GLY* 3.4 6.8 - - - -
190K ALA 2.8 34.8 + - - +
192K LEU* 3.9 28.0 - - + -
202K ASN* 4.1 2.1 + - - +
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Residues in contact with GLY 145 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26K VAL* 4.9 2.5 - - - -
66K SER* 3.2 17.0 - - - -
144K VAL* 1.3 76.4 - - - +
146K ASN* 1.3 59.9 + - - -
147K PRO* 3.4 7.2 - - - +
152K GLN* 3.5 5.3 - - - -
153K THR 2.8 33.4 + - - +
186K ASN* 3.6 14.9 + - - -
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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