Contacts of the helix formed by residues 137 - 145 (chain I) in PDB entry 3LUE
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 GLN 137 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11I ASP* 4.3 6.6 - - - +
12I ASN 4.0 17.7 + - - -
13I GLY* 5.9 1.4 - - - -
74I GLY* 5.1 4.2 + - - -
106I THR* 3.8 13.3 + - - +
107I GLU* 3.0 34.8 + - - +
108I ALA* 3.3 10.3 - - - +
109I PRO* 4.7 1.3 - - - +
136I ILE* 1.3 73.6 - - - +
138I ALA* 1.4 62.6 + - - +
140I LEU* 3.2 15.4 + - - +
141I SER 3.3 8.8 + - - -
154I ASP* 2.9 10.4 - - - +
156I GLY* 4.0 21.9 - - - -
157I ASP 5.0 2.3 + - - +
339I VAL* 3.4 37.2 - - + +
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Residues in contact with ALA 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I PRO* 4.8 0.4 - - + -
136I ILE* 3.5 9.2 - - + +
137I GLN* 1.4 69.7 - - - +
139I VAL* 1.3 62.2 + - - +
141I SER* 3.3 4.9 + - - -
142I LEU* 3.1 18.0 + - - +
152I VAL* 3.5 15.1 - - + +
154I ASP* 1.5 67.2 + - + +
161I HIS* 4.7 3.6 - - + +
163I VAL* 5.0 7.9 - - + -
300I SER* 3.6 1.3 - - - +
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Residues in contact with VAL 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G VAL 4.9 7.3 - - - +
45G VAL* 3.1 18.7 - - - +
135I ALA* 6.1 1.3 - - + -
136I ILE* 3.5 25.0 + - + +
137I GLN 3.3 1.0 - - - -
138I ALA* 1.3 77.1 - - - +
140I LEU* 1.3 59.9 + - + +
142I LEU* 3.6 5.0 - - - +
143I TYR* 3.3 9.7 + - + +
163I VAL* 3.6 38.1 - - + -
165I ILE* 5.7 0.4 - - + -
170I ALA* 4.8 7.2 - - + -
375I PHE* 4.7 21.5 - - + -
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Residues in contact with LEU 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I VAL* 5.2 0.4 - - + -
104I LEU* 3.9 6.1 - - + -
106I THR* 3.2 30.5 - - + -
135I ALA* 3.4 21.5 - - + -
136I ILE 2.9 30.1 - - - +
137I GLN 3.2 4.2 + - - +
139I VAL* 1.3 76.9 - - + +
141I SER* 1.3 65.4 + - - +
142I LEU 3.3 0.4 - - - -
143I TYR* 4.5 3.8 - - - +
144I ALA* 3.1 19.6 + - - +
338I SER 4.2 1.3 - - - -
339I VAL* 3.3 24.7 - - + +
342I GLY* 3.1 15.1 + - - +
343I GLY* 3.6 27.1 - - - +
346I LEU* 5.7 5.4 - - + -
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Residues in contact with SER 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G VAL* 2.4 22.3 - - - +
137I GLN 3.3 2.4 + - - -
138I ALA 3.3 6.4 + - - -
140I LEU* 1.3 76.9 - - - +
142I LEU* 1.3 53.9 + - - -
144I ALA* 3.5 3.3 + - - +
145I SER* 3.4 15.2 + - - -
154I ASP* 3.4 1.6 + - - -
300I SER* 2.8 41.7 + - - -
338I SER* 3.6 22.2 + - - -
339I VAL* 3.2 23.7 - - - +
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Residues in contact with LEU 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G VAL 3.1 2.0 - - - +
44G MET* 2.1 22.4 - - - -
45G VAL* 0.9 384.7 - - + +
47G MET 3.2 6.6 - - - +
138I ALA 3.1 5.3 + - - +
139I VAL 3.6 5.4 - - - +
141I SER* 1.3 66.9 - - - +
143I TYR* 1.3 61.9 + - - -
145I SER* 2.8 13.9 + - - -
152I VAL* 2.1 28.3 - - + -
165I ILE* 1.5 54.5 - - + -
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Residues in contact with TYR 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G GLN* 5.4 2.2 - - + -
42G GLY 3.4 16.2 - - - -
43G VAL* 3.6 21.8 + - + +
45G VAL* 1.9 12.3 - - - +
47G MET 3.6 7.8 - - - +
48G GLY* 4.3 1.2 - - - -
49G GLN* 0.5 204.5 + - + +
139I VAL* 3.3 13.2 + - + +
140I LEU* 4.1 7.2 - - - +
141I SER 3.6 0.2 - - - -
142I LEU 1.3 68.2 - - - +
144I ALA* 1.3 62.3 + - - +
145I SER 3.2 2.8 + - - -
168I GLY 4.7 0.2 - - - -
342I GLY 4.6 8.5 - - - +
345I ILE* 4.0 30.6 - - + +
346I LEU* 4.7 18.4 - - + -
349I LEU* 4.4 4.5 - - + -
101P PHE* 4.9 2.4 - - + +
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Residues in contact with ALA 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I LEU 3.1 19.9 + - - +
141I SER 3.8 5.2 - - - +
142I LEU 3.2 0.2 - - - -
143I TYR* 1.3 75.1 - - - +
145I SER* 1.3 57.0 + - - +
338I SER* 4.1 11.0 - - - +
341I ILE* 4.0 9.6 - - + +
342I GLY* 3.4 23.0 - - - +
345I ILE* 4.0 16.2 - - + +
100P ARG* 5.9 2.9 - - - +
101P PHE* 4.9 4.8 - - + -
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Residues in contact with SER 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G VAL* 2.7 12.4 - - - -
46G GLY* 2.7 34.4 + - - -
47G MET 3.5 13.2 - - - -
48G GLY* 4.2 2.9 - - - -
141I SER 3.4 8.4 + - - -
142I LEU 2.8 7.6 + - - -
143I TYR 4.0 1.8 - - - -
144I ALA* 1.3 79.6 - - - +
146I GLY* 1.3 62.6 + - - +
147I ARG* 1.9 16.2 + - - -
298I VAL* 5.7 4.5 - - - -
100P ARG* 4.9 2.7 - - - -
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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
------------------------------------------------------------
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