Contacts of the strand formed by residues 126 - 136 (chain L) in PDB entry 3IU3
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 126 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124H PHE* 5.7 0.9 - - - -
145H LYS* 4.7 12.9 - - - +
146H ASP* 5.4 2.0 + - - +
121L GLN* 2.8 42.1 + - - +
122L LEU* 3.7 3.4 + - - -
124L SER* 3.6 11.7 + - - -
125L GLY* 1.3 82.3 - - - +
127L ALA* 1.3 62.0 + - - +
177L THR* 5.3 6.5 - - + -
178L LEU 3.4 11.9 - - - +
179L SER* 4.7 4.9 - - - -
180L LYS 4.7 1.6 - - - -
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Residues in contact with ALA 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117L PRO* 3.8 24.5 - - + -
121L GLN* 3.8 3.4 - - - +
122L LEU* 4.2 5.4 - - + -
126L THR* 1.3 77.5 - - - +
128L SER* 1.3 62.8 + - - +
129L VAL* 4.2 1.8 - - - +
176L LEU 3.5 2.1 - - - +
177L THR* 3.5 1.2 - - - +
178L LEU* 2.6 42.9 + - + +
179L SER 4.8 1.3 - - - +
183L TYR* 3.9 31.0 - - + -
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Residues in contact with SER 128 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H LEU* 5.6 2.3 - - - +
143H LEU* 3.7 19.5 - - - +
145H LYS* 3.2 22.2 + - - -
115L PHE 4.3 1.4 - - - +
116L PRO 4.4 0.3 - - - -
117L PRO* 3.7 19.3 - - - +
121L GLN* 2.8 31.0 + - - +
127L ALA* 1.3 73.2 + - - +
129L VAL* 1.3 62.6 + - - +
130L VAL* 3.8 5.6 + - - +
175L THR* 3.9 15.0 - - - -
176L LEU 3.2 3.6 - - - -
177L THR* 3.5 7.1 + - - +
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Residues in contact with VAL 129 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114L ILE* 4.2 3.8 - - + -
115L PHE 3.6 15.0 - - - +
117L PRO* 3.9 19.5 - - + -
127L ALA* 5.0 2.0 - - + +
128L SER* 1.3 75.7 - - - +
130L VAL* 1.3 59.0 + - - +
145L TRP* 3.4 26.0 - - + -
175L THR* 3.3 2.8 - - - -
176L LEU* 2.7 54.8 + - + +
178L LEU* 6.3 0.9 - - + -
183L TYR* 4.6 11.2 - - + -
189L TYR* 4.6 13.2 - - + -
206L PHE* 3.6 24.7 - - + -
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Residues in contact with VAL 130 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H LEU* 4.0 34.8 - - + -
143H LEU* 4.5 9.4 - - + -
181H SER* 4.3 15.9 - - - +
114L ILE* 3.5 2.2 - - - -
115L PHE* 2.8 53.4 + - + -
128L SER 3.8 6.2 + - - +
129L VAL* 1.3 73.9 - - - +
131L CYS* 1.3 70.2 + - - +
132L LEU* 4.8 2.7 - - + +
145L TRP* 4.3 1.8 - - - -
173L SER* 4.5 11.7 - - - -
174L SER 3.5 4.5 - - - +
175L THR* 4.1 20.6 - - + +
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Residues in contact with CYS 131 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L VAL* 4.2 10.3 - - - -
113L PHE 3.4 11.4 - - - -
114L ILE* 4.5 3.1 - - + +
129L VAL 3.8 0.8 + - - -
130L VAL* 1.3 74.7 - - - +
132L LEU* 1.3 62.2 + - - +
133L LEU* 4.1 14.6 + - - +
145L TRP* 3.6 18.2 - - + -
172L LEU 3.9 0.2 - - - +
173L SER* 3.1 6.9 - - - -
174L SER* 2.7 41.9 + - - +
191L CYS* 2.1 48.2 - - + -
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Residues in contact with LEU 132 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139H ALA* 4.1 8.3 - - + -
168H PHE* 3.6 24.7 - - + -
183H VAL* 3.6 39.5 - - + -
185H THR* 5.4 0.9 - - + -
111L SER 3.3 4.7 - - - +
112L VAL* 3.4 3.6 - - - +
113L PHE* 2.7 65.8 + - + +
115L PHE* 4.3 8.5 - - + -
130L VAL* 4.1 3.3 - - + -
131L CYS* 1.3 73.4 - - - +
133L LEU* 1.3 78.5 + - - +
134L ASN* 3.9 12.3 - - + +
171L SER* 5.0 0.2 - - - -
172L LEU 3.3 15.7 - - - +
173L SER* 4.5 2.0 - - - +
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Residues in contact with LEU 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110L PRO* 4.2 15.7 - - + -
111L SER 3.4 3.8 - - - -
112L VAL* 4.7 3.4 - - + -
131L CYS* 4.1 11.4 - - - -
132L LEU* 1.3 79.1 - - - +
134L ASN* 1.3 59.4 + - - +
136L PHE* 3.4 17.9 - - + -
141L ALA* 4.2 18.6 - - + -
143L VAL* 3.7 29.8 - - + -
171L SER* 3.4 4.3 - - - -
172L LEU* 2.7 51.7 + - + +
193L VAL* 3.5 40.6 - - + -
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Residues in contact with ASN 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166H HIS* 3.2 16.4 + - - -
183H VAL* 5.0 1.6 - - - +
185H THR* 3.5 31.2 + - - +
110L PRO* 3.5 1.1 - - - +
111L SER* 2.9 35.0 + - - +
113L PHE* 3.9 21.7 - - + -
132L LEU* 4.3 13.5 - - + +
133L LEU* 1.3 71.9 - - - +
135L ASN* 1.3 93.3 + - - +
136L PHE* 3.8 1.8 - - - -
171L SER* 3.0 18.3 + - - -
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Residues in contact with ASN 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166H HIS* 3.0 34.0 + - - -
185H THR* 4.9 2.9 + - - -
108L ALA* 4.2 7.8 - - - +
109L ALA 3.7 11.6 - - - +
134L ASN* 1.3 92.1 + - - +
136L PHE* 1.3 56.5 + - - +
164L ASP* 5.9 0.8 - - - -
167L ASP* 4.6 9.4 + - - +
169L THR* 3.5 27.9 + - + +
170L TYR 3.0 13.2 + - - -
171L SER* 3.3 4.4 + - - -
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Residues in contact with PHE 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108L ALA* 3.1 15.9 - - - +
110L PRO* 3.6 34.5 - - + -
133L LEU* 3.4 34.1 - - + -
135L ASN* 1.3 73.9 - - - +
137L TYR* 1.3 61.2 + - - +
138L PRO 3.0 28.5 - - - -
139L ARG* 3.3 19.5 - - - -
141L ALA* 4.4 7.4 - - + -
160L VAL* 5.3 2.2 - - + -
169L THR* 3.5 4.6 - - - -
170L TYR* 2.8 55.9 + - + -
171L SER 4.5 0.7 - - - -
172L LEU* 3.9 23.3 - - + -
195L HIS* 3.5 10.1 - + + -
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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