Contacts of the helix formed by residues 125 - 141 (chain A) in PDB entry 3LKB
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 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A MET* 3.0 16.2 - - - -
108A ILE* 3.8 30.2 - - - +
121A LEU* 4.7 4.2 - - - +
123A THR 4.5 0.7 - - - -
124A THR* 1.3 75.9 - - - +
126A TYR* 1.3 63.4 + - - +
127A SER* 3.6 8.2 + - - -
128A GLU* 3.1 24.4 + - - +
129A GLN* 3.1 27.7 + - - +
351A THR* 5.5 1.0 - - - +
378A PHE* 3.8 10.0 - - - -
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Residues in contact with TYR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A THR* 3.8 6.7 - - - -
106A MET* 2.8 52.7 + - + +
107A HIS* 3.6 11.9 - - + -
125A SER* 1.3 71.2 - - - +
127A SER* 1.3 58.1 + - - +
129A GLN* 3.3 17.3 - - - +
130A VAL* 2.9 33.1 + - - +
155A PHE* 3.8 7.4 - + - -
158A ALA* 3.7 11.9 - - + -
159A PRO* 3.8 14.1 - - + -
205A GLN* 3.1 35.9 - - - +
230A ALA* 4.8 0.6 - - + +
231A HIS* 5.2 1.1 - - + -
232A TYR* 3.2 34.0 - + - -
393A VAL* 2.8 35.5 - - + +
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Residues in contact with SER 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A HIS* 5.1 1.4 - - - -
108A ILE* 4.0 11.5 - - - +
125A SER* 3.2 4.8 + - - -
126A TYR* 1.3 74.9 - - - +
128A GLU* 1.3 60.4 + - - +
130A VAL* 3.3 1.6 + - - +
131A VAL* 2.9 35.0 + - - +
158A ALA 4.0 3.5 + - - -
159A PRO* 3.6 22.7 - - - +
162A ASP* 2.7 35.5 + - - -
378A PHE* 3.6 17.5 - - - -
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Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A THR* 4.0 21.7 - - - +
125A SER* 3.1 20.1 + - - +
127A SER* 1.3 78.8 - - - +
129A GLN* 1.3 53.3 + - - +
131A VAL* 3.6 1.2 - - - +
132A ALA* 2.7 36.7 + - - +
351A THR* 5.9 1.7 - - - +
354A GLU* 4.2 3.9 - - - +
356A LEU* 4.1 12.1 - - + -
374A THR* 3.5 6.9 - - - -
375A SER* 2.7 39.4 + - - +
378A PHE* 3.7 26.2 - - + -
379A ARG* 2.8 26.3 + - - -
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Residues in contact with GLN 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A MET* 3.7 15.0 - - - -
123A THR* 4.5 1.6 + - - -
124A THR* 3.1 42.2 + - - +
125A SER 3.1 10.5 + - - +
126A TYR* 3.3 14.5 - - - +
128A GLU* 1.3 76.1 - - - +
130A VAL* 1.3 58.1 + - - +
132A ALA* 3.2 3.1 + - - +
133A LEU* 3.0 34.5 + - - +
230A ALA* 3.5 13.3 - - + +
231A HIS* 2.9 34.5 + - - +
252A ALA* 4.0 16.8 - - + +
253A THR* 4.9 3.0 - - - +
254A SER 5.3 0.8 - - - +
356A LEU* 3.8 15.0 - - + -
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A TYR 2.9 23.2 + - - +
127A SER 3.9 2.2 - - - +
129A GLN* 1.3 73.8 - - - +
131A VAL* 1.3 57.0 + - - +
133A LEU* 3.3 10.0 + - + +
134A LEU* 3.0 30.5 + - + +
148A LEU* 5.2 3.6 - - + -
159A PRO* 3.9 24.9 - - + -
163A ALA* 3.7 30.3 - - + +
203A VAL* 4.4 24.9 - - + +
205A GLN* 5.2 4.5 - - + +
230A ALA* 4.4 15.7 - - + -
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Residues in contact with VAL 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A SER 2.9 25.2 + - - +
128A GLU 3.8 2.7 - - - +
130A VAL* 1.3 68.7 - - + +
132A ALA* 1.3 65.3 + - - +
134A LEU* 3.8 8.1 - - - +
135A GLU* 3.0 22.9 + - - +
162A ASP* 3.9 20.6 - - + +
163A ALA* 4.7 2.2 - - - +
166A ALA* 3.8 22.0 - - + -
375A SER* 3.7 7.9 - - - +
377A LEU* 3.8 19.3 - - + -
378A PHE* 3.6 34.5 - - + +
381A VAL* 4.6 0.9 - - + -
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Residues in contact with ALA 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU 2.7 21.2 + - - +
129A GLN* 3.2 5.6 + - - +
131A VAL* 1.3 72.0 - - - +
133A LEU* 1.3 62.9 + - - +
135A GLU* 3.2 14.4 + - - +
136A TYR* 3.1 20.8 + - - +
356A LEU* 4.0 15.0 - - + -
358A ILE* 4.4 7.4 - - + +
373A PHE* 3.8 32.0 - - + -
375A SER* 4.7 6.0 + - - -
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLN 3.0 18.1 + - - +
130A VAL* 3.4 14.4 - - + +
132A ALA* 1.3 73.6 - - - +
134A LEU* 1.3 59.7 + - - +
136A TYR* 3.2 7.3 + - + +
137A ILE* 2.8 32.7 + - - +
203A VAL* 4.3 13.7 - - + -
228A LEU* 4.0 21.3 - - + +
229A GLY* 3.5 36.3 - - - +
230A ALA* 4.0 2.5 - - - +
250A LEU 4.0 17.9 - - - +
252A ALA* 3.9 11.9 - - + +
358A ILE* 3.7 27.4 - - + -
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 3.0 20.7 + - + +
131A VAL* 3.3 8.0 + - - +
133A LEU* 1.3 72.5 - - - +
135A GLU* 1.3 65.6 + - - +
137A ILE* 3.1 23.9 + - + +
138A ALA 2.9 19.1 + - - -
146A VAL* 4.1 18.2 - - + -
148A LEU* 5.1 2.7 - - + -
163A ALA* 3.5 42.8 - - + +
166A ALA* 4.1 11.9 - - + -
167A ALA* 4.2 7.4 - - + +
170A LEU* 3.7 15.4 - - + +
172A LEU* 3.6 19.4 - - + +
174A ILE* 4.8 4.5 - - + -
203A VAL* 4.4 7.4 - - + -
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Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A VAL 3.0 14.1 + - - +
132A ALA* 3.4 11.2 - - - +
133A LEU 3.2 0.2 - - - -
134A LEU* 1.3 74.9 - - - +
136A TYR* 1.3 63.7 + - - +
138A ALA* 3.0 3.8 + - - +
139A ARG* 3.0 23.7 + - - +
170A LEU* 4.0 13.1 - - + +
373A PHE* 4.9 7.9 - - + -
375A SER* 2.9 34.3 + - - -
376A ALA 4.9 0.2 + - - -
377A LEU* 3.8 30.6 + - + +
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Residues in contact with TYR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ALA 3.1 9.4 + - - +
133A LEU* 3.3 12.3 - - + +
135A GLU* 1.3 79.2 - - - +
137A ILE* 1.3 61.9 + - - +
139A ARG* 2.4 58.8 - - - +
140A GLU* 3.3 27.3 + - + +
201A TYR* 6.2 1.3 - + - -
226A ARG* 5.7 0.7 + - - -
228A LEU* 4.5 6.1 - - + -
250A LEU* 3.4 39.2 - - + +
358A ILE* 4.4 22.4 - - + -
360A GLU* 5.5 1.7 + - - -
369A VAL* 4.5 20.7 - - + +
370A THR* 5.1 8.1 - - + -
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU 2.8 21.7 + - - +
134A LEU* 3.1 20.2 + - + +
136A TYR* 1.3 75.5 - - - +
138A ALA* 1.3 57.4 + - - +
140A GLU* 3.1 9.0 + - - +
141A LYS* 3.0 24.4 + - - +
144A ALA* 3.7 27.1 - - + -
146A VAL* 4.6 5.2 - - + -
172A LEU* 4.1 10.8 - - + -
201A TYR* 3.6 41.1 - - + -
203A VAL* 3.7 29.6 - - + -
228A LEU* 3.8 12.6 - - + -
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LEU 2.9 15.2 + - - +
135A GLU 3.0 6.3 + - - +
137A ILE* 1.3 69.7 - - - +
139A ARG* 1.3 61.2 + - - +
140A GLU 3.4 0.2 + - - -
141A LYS 3.5 13.7 + - - -
142A LYS* 2.9 25.6 + - - +
170A LEU* 4.0 30.5 - - + +
172A LEU* 3.8 18.6 - - + -
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Residues in contact with ARG 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLU 3.0 9.1 + - - +
136A TYR* 2.4 66.9 - - - +
138A ALA* 1.3 77.7 - - - +
140A GLU* 1.3 76.4 + - - +
142A LYS* 3.0 15.6 + - - +
370A THR* 5.4 8.3 - - - +
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Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A TYR* 3.9 26.8 + - + +
137A ILE* 3.1 10.2 + - - +
139A ARG* 1.3 101.5 - - - +
141A LYS* 1.3 60.2 + - - +
142A LYS* 3.8 5.1 + - - -
201A TYR* 2.8 36.0 + - + +
226A ARG* 4.9 15.2 + - - -
250A LEU* 6.1 0.4 - - - -
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ILE 3.0 9.3 + - - +
138A ALA* 3.7 7.0 - - - +
139A ARG 3.5 1.4 - - - -
140A GLU* 1.3 81.4 - - - +
142A LYS* 1.3 76.6 + - - +
143A GLY 3.8 1.0 + - - -
144A ALA* 3.3 28.6 + - + +
172A LEU* 4.1 0.3 - - - +
200A GLU* 2.9 34.8 + - - +
201A TYR* 3.7 20.9 - - + +
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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) + - + + + + + -
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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