Contacts of the helix formed by residues 124 - 138 (chain A) in PDB entry 6EKK
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 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A ASP* 4.6 4.9 - - - +
119A TYR* 2.7 44.7 + - + +
122A LYS* 3.5 29.1 - - + +
123A ARG* 1.3 69.6 - - - +
125A GLU* 1.3 64.3 + - - +
126A ASN 3.3 3.4 - - - -
127A GLN* 3.2 38.5 + - - +
128A TRP* 3.2 22.9 + - - +
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Residues in contact with GLU 125 (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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35A ARG* 2.5 41.4 + - - +
119A TYR 4.9 1.2 - - - +
120A THR* 5.0 0.5 - - - +
123A ARG* 3.2 24.3 + - + +
124A GLN* 1.3 75.8 - - - +
126A ASN* 1.3 62.7 + - - +
128A TRP* 3.5 4.9 - - - +
129A ASN* 3.0 39.2 + - - +
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Residues in contact with ASN 126 (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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124A GLN 3.3 0.6 - - - -
125A GLU* 1.3 80.1 + - - +
127A GLN* 1.3 69.6 + - - +
129A ASN* 3.5 7.1 + - - +
130A GLU* 2.9 30.1 + - - +
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Residues in contact with GLN 127 (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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119A TYR* 3.5 37.7 - - + +
124A GLN* 3.2 37.8 + - - +
126A ASN* 1.3 82.7 + - - +
128A TRP* 1.3 66.4 + - - +
130A GLU* 3.9 5.4 - - - +
131A LEU* 3.0 27.4 + - - +
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Residues in contact with TRP 128 (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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16A TYR* 3.4 42.4 + + - -
35A ARG* 3.2 48.2 - - + +
36A GLN 3.9 21.3 - - - -
37A PHE* 4.1 4.9 - + + -
116A LEU* 3.6 24.6 - - + +
119A TYR* 3.6 12.9 - - + -
120A THR* 3.8 18.9 + - - -
124A GLN 3.2 18.9 + - - +
125A GLU 3.5 3.6 - - - +
127A GLN* 1.3 79.4 - - - +
129A ASN* 1.3 98.5 + - - +
131A LEU* 3.8 1.6 - - - +
132A LEU* 3.2 41.3 + - + +
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Residues in contact with ASN 129 (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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37A PHE* 3.8 17.4 - - - -
125A GLU* 3.0 27.8 + - - +
126A ASN* 3.8 8.1 - - - +
128A TRP* 1.3 99.9 - - - +
130A GLU* 1.3 57.3 + - - +
132A LEU* 4.1 2.6 - - - +
133A GLU* 2.9 34.6 + - - +
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Residues in contact with GLU 130 (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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126A ASN 2.9 19.7 + - - +
127A GLN* 3.9 6.1 - - - +
129A ASN* 1.3 76.7 - - - +
131A LEU* 1.3 58.5 + - - +
133A GLU* 4.0 3.7 - - - +
134A THR* 2.9 37.9 + - - +
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Residues in contact with LEU 131 (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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112A LEU* 3.9 29.8 - - + -
115A ILE* 3.7 32.3 - - + -
116A LEU* 3.9 21.3 - - + -
119A TYR* 4.2 5.4 - - + +
127A GLN 3.0 17.3 + - - +
128A TRP 3.8 2.9 - - - +
130A GLU* 1.3 77.0 - - - +
132A LEU* 1.3 58.2 + - + +
134A THR* 3.8 5.5 - - + -
135A LEU* 2.9 36.3 + - + +
148A HIS 5.1 3.4 - - - +
149A LEU* 4.2 24.5 - - + +
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Residues in contact with LEU 132 (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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13A PHE* 3.7 25.2 - - + -
16A TYR* 3.8 19.1 - - + -
37A PHE* 3.7 31.0 - - + -
99A ILE* 4.9 4.3 - - + -
116A LEU* 3.8 27.1 - - + -
128A TRP* 3.2 57.0 + - + +
129A ASN 4.1 0.2 - - - +
131A LEU* 1.3 79.7 - - + +
133A GLU* 1.3 58.8 + - - +
135A LEU* 3.7 6.0 - - + -
136A HIS* 2.8 32.2 + - - +
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Residues in contact with GLU 133 (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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37A PHE* 3.6 21.8 - - + -
129A ASN 2.9 20.5 + - - +
130A GLU* 4.0 4.0 - - - +
132A LEU* 1.3 73.5 - - - +
134A THR* 1.3 67.3 + - - +
136A HIS* 3.9 8.5 + - - +
137A LYS* 3.0 30.4 + - + +
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Residues in contact with THR 134 (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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130A GLU* 2.9 25.9 + - - +
131A LEU* 3.8 6.5 - - + -
133A GLU* 1.3 78.8 - - - +
135A LEU* 1.3 64.8 + - - +
137A LYS* 3.9 4.0 - - - +
138A LEU* 3.1 27.6 + - + +
148A HIS 6.0 2.2 - - - +
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Residues in contact with LEU 135 (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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12A THR* 2.7 38.9 + - + +
13A PHE* 3.8 18.8 - - + -
99A ILE* 4.5 9.0 - - + -
105A TRP* 6.2 2.5 - - + -
108A VAL* 6.2 0.2 - - + -
109A PHE* 4.5 4.5 - - + -
112A LEU* 3.7 40.4 - - + -
116A LEU* 6.1 1.1 - - + -
131A LEU* 2.9 22.6 + - + +
132A LEU* 3.8 9.0 - - + +
134A THR* 1.3 78.6 - - - +
136A HIS* 1.3 57.9 + - - +
138A LEU* 3.1 28.7 + - + +
155A PHE* 5.3 12.1 - - + -
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Residues in contact with HIS 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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11A THR* 4.2 30.7 + - + +
12A THR* 3.8 2.8 + - - -
13A PHE* 3.3 52.8 + + + -
14A GLU* 4.2 3.4 + - - -
37A PHE* 4.0 10.6 - + + -
38A PRO* 3.8 26.5 - - + +
132A LEU 2.8 21.9 + - - +
133A GLU* 3.9 8.9 + - - +
135A LEU* 1.3 73.7 - - - +
137A LYS* 1.3 60.0 + - - +
138A LEU 3.7 2.3 + - - +
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Residues in contact with LYS 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 GLU* 3.0 24.8 + - + +
134A THR* 4.0 4.5 - - - +
135A LEU 3.2 0.2 - - - -
136A HIS* 1.3 76.7 - - - +
138A LEU* 1.3 64.1 + - - +
139A PRO* 3.2 9.9 - - - +
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Residues in contact with LEU 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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10A GLU 5.6 0.5 - - - +
11A THR* 5.5 1.7 - - - -
12A THR* 3.6 23.2 + - + +
105A TRP* 6.5 0.9 - - + -
134A THR* 3.1 17.2 + - + +
135A LEU* 3.1 24.9 + - + +
136A HIS 4.5 2.4 - - - +
137A LYS* 1.3 76.7 - - - +
139A PRO* 1.3 86.2 - - + +
140A ILE* 3.4 3.6 + - - +
141A PRO* 4.0 25.6 - - + -
147A VAL* 4.6 17.3 - - + -
155A PHE* 5.9 1.3 - - + -
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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