Contacts of the strand formed by residues 123 - 130 (chain U) in PDB entry 3LAQ
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 CYS 123 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94U LEU* 4.4 7.9 - - - -
95U GLU 3.7 10.3 - - - -
96U CYS* 2.1 44.6 - - - -
122U HIS* 1.3 75.0 - - - +
124U ILE* 1.3 66.5 + - - +
144U GLY 3.7 0.7 - - - -
167U LYS 3.8 0.2 - - - +
168U CYS* 3.2 0.7 - - - -
169U CYS* 2.9 32.7 + - - -
171U TYR 3.7 17.9 - - - -
174U CYS* 3.3 17.9 - - - -
175U ASN* 3.0 17.9 - - - +
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Residues in contact with ILE 124 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U THR 5.1 1.1 - - - +
55U MET* 5.2 15.0 - - + -
123U CYS* 1.3 83.0 - - - +
125U GLU* 1.3 63.6 + - - +
126U VAL* 5.2 4.5 - - + -
142U THR* 3.9 0.4 - - + +
143U ARG* 3.2 6.8 - - - +
144U GLY* 2.8 52.1 + - - +
145U CYS 3.1 11.4 - - - +
146U GLY* 3.0 48.5 - - - +
148U LEU* 5.0 11.7 - - + -
151U CYS* 4.3 2.5 - - - -
166U LEU* 4.2 11.4 - - + -
167U LYS 3.1 12.6 - - - +
168U CYS* 3.5 18.2 - - + -
175U ASN* 3.6 7.7 + - - +
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Residues in contact with GLU 125 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124U ILE* 1.3 73.8 - - - +
126U VAL* 1.3 61.3 + - - +
127U VAL 4.3 0.2 - - - -
141U TYR* 5.1 5.9 - - - +
142U THR 3.3 3.2 + - - +
143U ARG* 2.8 61.8 + - + +
165U PHE* 4.0 1.4 - - + +
166U LEU* 3.4 4.9 - - - +
167U LYS* 2.8 49.4 + - + +
175U ASN* 4.2 13.8 - - + +
176U GLY 5.1 0.3 - - - +
178U PRO 4.4 1.7 - - - +
179U VAL* 3.8 13.0 - - - +
180U LEU* 3.2 31.3 - - + +
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Residues in contact with VAL 126 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LYS* 3.0 32.5 - - - +
25A TYR* 4.1 14.4 - - + +
55U MET* 4.6 16.2 - - + -
124U ILE* 5.2 6.3 - - + -
125U GLU* 1.3 76.7 - - - +
127U VAL* 1.3 62.2 - - - +
128U THR* 4.2 1.5 + - - +
138U ASP* 5.9 0.9 - - - +
139U GLU 5.1 1.3 - - - +
140U ASP 3.5 3.6 - - - +
141U TYR* 3.6 0.7 - - - -
142U THR* 2.8 58.6 + - + +
148U LEU* 5.5 1.8 - - + -
165U PHE 3.5 4.7 - - - +
166U LEU* 4.5 6.1 - - + +
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Residues in contact with VAL 127 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LYS* 4.5 2.4 + - - -
125U GLU* 6.0 0.4 - - + -
126U VAL* 1.3 74.8 - - - +
128U THR* 1.3 65.9 + - - +
129U LEU* 3.8 18.4 - - + -
140U ASP 3.2 2.9 - - - +
141U TYR* 3.2 35.9 - - + -
163U PHE* 3.9 17.9 - - + -
164U HIS* 3.2 5.5 - - - +
165U PHE* 2.7 77.9 + - + +
180U LEU* 4.3 10.5 - - + +
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Residues in contact with THR 128 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LYS* 3.3 32.1 + - - +
126U VAL* 4.2 1.6 + - - +
127U VAL* 1.3 71.8 + - - +
129U LEU* 1.3 64.4 + - - +
130U GLN* 4.0 27.7 + - + +
136U LEU* 4.2 11.0 - - + -
138U ASP* 4.4 8.0 + - + +
139U GLU 3.7 13.4 + - - +
140U ASP* 2.8 32.9 + - - +
162U THR* 5.8 0.2 - - + -
163U PHE 3.6 2.9 - - - -
164U HIS* 3.6 20.8 - - + +
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Residues in contact with LEU 129 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127U VAL* 3.8 22.0 - - + -
128U THR* 1.3 81.7 - - - +
130U GLN* 1.3 61.1 + - - +
140U ASP* 3.7 26.0 - - + +
141U TYR* 3.9 23.1 - - + +
161U GLN 4.6 0.2 - - - -
162U THR* 3.3 9.5 - - - +
163U PHE* 2.8 61.6 + - + +
180U LEU 5.0 0.9 - - - +
181U ASP* 5.1 6.3 - - + -
182U LEU* 5.2 5.2 - - + +
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Residues in contact with GLN 130 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128U THR* 4.0 17.6 + - + +
129U LEU* 1.3 77.7 - - - +
131U SER* 1.3 62.0 + - - +
134U ARG* 3.2 47.9 + - + +
135U SER 4.2 1.4 + - - +
136U LEU* 2.9 56.7 + - - +
138U ASP 3.7 19.4 + - - +
140U ASP* 5.0 6.5 + - - +
161U GLN 3.7 6.3 - - - -
162U THR* 4.4 9.3 - - + +
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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