Contacts of the helix formed by residues 133 - 155 (chain L) in PDB entry 3CX5
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 133 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81L GLU* 4.5 6.1 + - - -
129L ALA 4.1 2.0 + - - -
130L ASN 3.9 13.7 + - - -
131L LEU 3.3 1.6 - - - -
132L LEU* 1.3 79.9 - - - +
134L SER* 1.3 58.4 + - - +
135L SER* 4.2 5.2 + - - -
136L ASN* 3.1 22.7 + - - +
137L PHE* 2.7 31.1 + - - +
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Residues in contact with SER 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132L LEU 3.9 1.4 + - - -
133L SER* 1.3 71.0 - - - +
135L SER* 1.3 58.6 + - - +
137L PHE* 4.7 4.0 - - - -
138L GLU* 3.0 41.1 + - - +
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Residues in contact with SER 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81L GLU* 5.7 2.9 - - - -
133L SER* 3.2 5.5 + - - -
134L SER* 1.3 78.5 - - - +
136L ASN* 1.3 62.3 + - - +
138L GLU* 4.3 2.7 - - - +
139L ALA* 3.2 25.6 + - - +
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Residues in contact with ASN 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76L ILE* 4.4 6.5 - - - +
79L SER* 2.6 35.9 + - - -
81L GLU* 3.7 29.2 + - - +
131L LEU* 2.8 32.4 + - - +
133L SER* 3.1 20.1 + - - +
135L SER* 1.3 75.7 - - - +
137L PHE* 1.3 61.8 + - - +
139L ALA* 3.5 4.0 + - - +
140L THR* 2.9 35.7 + - - -
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Residues in contact with PHE 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L LEU* 4.0 13.7 - - + -
76L ILE* 4.9 10.8 - - + -
131L LEU 4.5 1.2 + - - -
132L LEU* 4.7 11.9 - - + +
133L SER 2.7 21.5 + - - +
134L SER* 4.0 3.8 - - - +
136L ASN* 1.3 73.2 - - - +
138L GLU* 1.3 73.9 + - + +
140L THR* 3.3 4.5 + - - -
141L LYS* 2.8 54.7 + - + +
188L LEU 3.4 28.5 - - - -
189L VAL* 3.7 16.6 - - + -
190L VAL* 3.6 28.0 - - + -
193L LEU* 3.6 31.0 - - + -
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Residues in contact with GLU 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134L SER* 3.0 27.4 + - - +
135L SER* 4.3 2.9 - - - +
137L PHE* 1.3 94.0 - - + +
139L ALA* 1.3 58.2 + - - +
141L LYS* 3.7 17.3 + - - +
142L LYS* 3.0 29.3 + - - +
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Residues in contact with ALA 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135L SER 3.2 19.6 + - - +
136L ASN* 3.9 6.5 - - - +
138L GLU* 1.3 73.6 - - - +
140L THR* 1.3 66.2 + - - +
142L LYS* 3.4 9.2 + - - +
143L SER* 3.1 25.5 + - - -
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Residues in contact with THR 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L LEU* 4.2 7.6 - - + +
75L ASN* 3.6 34.3 + - + +
76L ILE* 3.6 29.0 - - + +
79L SER* 3.9 14.9 + - - -
136L ASN* 2.9 22.3 + - - -
137L PHE* 3.7 3.6 - - + -
139L ALA* 1.3 74.7 - - - +
141L LYS* 1.3 65.5 + - - +
143L SER* 2.9 17.3 + - - -
144L VAL* 3.0 15.8 + - + +
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Residues in contact with LYS 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72L LEU* 4.5 9.9 - - + -
137L PHE* 2.8 49.9 + - + +
138L GLU* 3.9 16.8 + - - +
140L THR* 1.3 72.7 - - - +
142L LYS* 1.3 62.0 + - - +
144L VAL* 3.1 26.4 - - + +
145L LEU* 3.1 20.7 + - + +
185L LEU* 3.4 24.2 - - + +
186L GLU* 2.9 29.4 + - - +
187L ASN 4.5 0.4 - - - -
188L LEU* 2.9 20.1 + - + +
189L VAL* 5.3 2.4 - - - +
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Residues in contact with LYS 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138L GLU 3.0 20.4 + - - +
139L ALA* 3.5 9.4 - - - +
140L THR 3.1 0.2 - - - -
141L LYS* 1.3 77.8 - - - +
143L SER* 1.3 61.3 + - - +
145L LEU* 3.6 11.5 - - + +
146L LYS* 3.3 19.9 + - - +
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Residues in contact with SER 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75L ASN* 5.6 1.1 - - - -
139L ALA 3.1 13.1 + - - -
140L THR* 2.9 12.0 + - - -
142L LYS* 1.3 76.3 - - - +
144L VAL* 1.3 61.0 + - - +
146L LYS* 3.1 8.7 + - - +
147L GLN* 3.0 40.3 + - - +
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Residues in contact with VAL 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71L ASN* 4.4 13.7 - - - +
72L LEU* 3.3 33.7 - - + -
75L ASN* 3.4 43.5 - - + +
140L THR* 3.0 13.4 + - + +
141L LYS* 3.1 14.8 - - + +
143L SER* 1.3 73.0 - - - +
145L LEU* 1.3 64.1 + - - +
147L GLN* 3.2 8.8 + - - +
148L VAL* 2.9 37.4 + - + +
185L LEU* 4.5 10.3 - - + -
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Residues in contact with LEU 145 (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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141L LYS* 3.1 26.9 + - + +
142L LYS* 3.6 10.8 - - + +
143L SER 3.2 0.2 - - - -
144L VAL* 1.3 81.0 - - - +
146L LYS* 1.3 57.7 + - - +
148L VAL* 4.8 0.4 - - - -
149L GLN* 3.1 27.7 + - - +
182L LEU* 3.7 26.7 - - + +
185L LEU* 3.6 33.0 - - + -
186L GLU* 3.9 30.3 - - + +
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Residues in contact with LYS 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142L LYS 3.3 10.1 + - - +
143L SER* 3.1 11.7 + - - +
145L LEU* 1.3 78.5 - - - +
147L GLN* 1.3 65.8 + - + +
149L GLN* 3.4 22.2 + - - +
150L ASP* 3.0 38.1 + - - +
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Residues in contact with GLN 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71L ASN* 5.1 5.6 + - - +
75L ASN* 3.2 31.4 + - - +
143L SER* 3.0 30.7 + - - +
144L VAL* 3.2 11.2 + - - +
146L LYS* 1.3 78.0 - - + +
148L VAL* 1.3 59.5 + - + +
150L ASP* 3.2 8.1 + - - +
151L PHE* 2.9 28.1 + - - +
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Residues in contact with VAL 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71L ASN* 4.2 8.3 - - - +
144L VAL 2.9 20.0 + - - +
147L GLN* 1.3 74.8 - - + +
149L GLN* 1.3 65.1 + - - +
151L PHE* 3.4 8.1 + - + +
152L GLU* 3.0 35.3 + - - +
179L ARG* 3.8 26.7 - - + +
180L GLY 4.0 17.5 - - - +
182L LEU* 3.7 27.6 - - + +
185L LEU* 3.7 21.5 - - + -
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Residues in contact with GLN 149 (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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145L LEU 3.1 19.8 + - - +
146L LYS* 3.7 24.4 - - - +
148L VAL* 1.3 76.1 - - - +
150L ASP* 1.3 58.1 + - - +
152L GLU* 3.5 2.0 + - - +
153L ASP* 3.0 50.0 + - - +
182L LEU* 3.8 22.7 - - + +
306O LYS* 4.2 17.8 + - - +
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Residues in contact with ASP 150 (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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146L LYS* 3.0 32.2 + - - +
147L GLN* 3.3 12.1 - - - +
149L GLN* 1.3 77.1 + - - +
151L PHE* 1.3 57.9 + - - +
153L ASP* 3.2 1.0 + - - -
154L ASN* 2.7 66.5 + - - +
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Residues in contact with PHE 151 (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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147L GLN 2.9 16.1 + - - +
148L VAL* 3.6 8.5 - - + +
150L ASP* 1.3 74.8 - - - +
152L GLU* 1.3 76.1 + - - +
155L ASP* 2.9 50.7 + - + +
158L ASN* 3.6 41.1 - - + -
159L ARG* 3.8 15.1 - - - +
162L GLU* 4.7 7.0 - - + -
179L ARG* 3.3 59.2 - - + +
34P TYR* 4.1 13.7 - - - -
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Residues in contact with GLU 152 (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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148L VAL* 3.0 29.3 + - - +
149L GLN* 3.8 6.5 - - - +
151L PHE* 1.3 93.7 - - - +
153L ASP* 1.3 64.3 + - - +
159L ARG* 3.4 39.5 + - - +
163L HIS* 3.9 8.9 - - + -
180L GLY 5.0 2.4 - - - +
181L THR* 5.9 0.7 - - - -
182L LEU* 5.3 11.8 - - + +
33P THR* 5.9 1.6 - - - +
34P TYR* 2.7 42.8 + - + -
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Residues in contact with ASP 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L GLN* 3.0 31.3 + - - +
150L ASP* 3.9 2.4 - - - +
152L GLU* 1.3 83.0 - - - +
154L ASN* 1.3 75.0 + - - +
156L HIS* 3.3 16.4 + - - -
159L ARG* 5.2 0.3 + - - -
256L LEU* 5.7 0.7 - - - +
306O LYS* 3.3 31.3 + - - -
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Residues in contact with ASN 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150L ASP* 2.7 50.8 + - - +
151L PHE 3.4 0.2 + - - -
153L ASP* 1.3 90.1 - - - +
155L ASP* 1.3 58.9 + - - +
156L HIS* 3.1 24.7 + - - -
157L PRO* 5.3 0.3 - - - +
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Residues in contact with ASP 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150L ASP 4.0 0.4 + - - -
151L PHE* 2.9 39.9 + - + +
154L ASN* 1.3 70.0 - - - +
156L HIS* 1.3 56.3 + - - +
157L PRO* 3.7 9.1 - - - +
158L ASN* 2.9 45.8 + - - +
159L ARG* 2.8 33.1 + - - +
179L ARG* 5.3 1.0 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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