Contacts of the strand formed by residues 136 - 142 (chain F) in PDB entry 3QAZ
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 GLU 136 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134F ALA 3.6 9.4 - - - +
135F PRO* 1.3 79.5 - - - +
137F ASN* 1.3 85.8 + - - +
138F LEU* 3.5 5.2 - - - -
152F TRP* 3.6 2.1 - - - +
153F ASN* 3.2 28.6 + - + +
154F ASN* 5.7 0.2 - - - +
155F ARG* 2.7 53.6 + - + +
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Residues in contact with ASN 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F GLU* 1.3 93.5 + - - +
138F LEU* 1.3 65.6 + - - +
139F THR* 3.5 17.1 + - + +
152F TRP* 3.8 9.4 - - - -
153F ASN* 4.3 17.8 + - - +
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Residues in contact with LEU 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F PRO 3.9 10.1 - - - +
136F GLU* 3.9 9.0 - - - +
137F ASN* 1.3 75.0 - - - +
139F THR* 1.3 65.7 + - - +
150F LEU* 5.0 4.7 - - + -
151F ASN 3.5 8.1 - - - +
152F TRP* 4.4 8.1 - - + -
199F PHE* 3.7 22.2 - - + +
200F ARG* 3.8 7.4 - - - -
201F VAL* 4.0 13.9 - - + -
219F SER* 2.9 39.5 - - - +
220F HIS* 3.3 18.8 - - + +
222F ILE* 3.2 36.8 - - + +
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Residues in contact with THR 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F ASN* 3.7 16.4 + - + +
138F LEU* 1.3 80.7 - - - +
140F LEU* 1.3 65.2 + - - +
141F HIS* 4.8 0.8 - - - +
149F GLU 3.9 0.2 - - - +
150F LEU* 3.9 2.3 - - - +
151F ASN* 3.2 45.5 + - - +
222F ILE* 3.4 4.2 - - - +
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Residues in contact with LEU 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F THR* 1.3 75.8 - - - +
141F HIS* 1.3 61.5 + - - +
148F LEU* 4.2 16.6 - - + -
149F GLU 3.7 1.8 - - - +
150F LEU* 3.4 29.6 - - + -
199F PHE* 3.5 27.1 - - + -
222F ILE* 3.5 13.3 - - + +
223F HIS 3.7 16.2 - - - +
224F TRP* 3.2 53.4 - - + -
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Residues in contact with HIS 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F THR* 4.8 1.1 - - - +
140F LEU* 1.3 76.2 - - - +
142F LYS* 1.3 93.9 + - - +
143F LEU* 5.1 4.2 - - + +
148F LEU* 4.2 1.6 - - - -
149F GLU* 2.5 59.3 + - + +
151F ASN* 4.4 11.7 - - - +
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Residues in contact with LYS 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F HIS* 1.3 97.6 + - - +
143F LEU* 1.3 60.4 + - - +
144F SER 3.5 21.3 - - - +
145F GLU* 4.0 27.8 + - - +
147F GLN 3.7 3.1 - - - +
148F LEU* 3.6 21.5 - - + -
191F VAL* 5.9 2.7 - - + -
224F TRP* 4.2 30.6 - - + -
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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