Contacts of the helix formed by residues 113 - 130 (chain A) in PDB entry 4DKE
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 HIS 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A TYR* 3.6 23.0 + - + -
58A PHE* 4.6 7.5 - + - -
109A LEU* 3.4 41.2 - - + +
110A LEU 3.3 16.2 + - - +
111A GLU 3.1 2.5 - - - +
112A GLY* 1.3 77.4 - - - +
114A PRO* 1.3 76.3 - - + +
115A SER* 3.1 39.2 + - - -
116A TRP* 2.9 21.8 + - + +
117A LYS* 4.2 0.5 + - - +
56B HIS 3.3 19.5 + - - +
57B TYR 3.4 28.8 + - - -
58B PHE* 4.0 8.0 - - - -
59B PRO* 5.0 1.0 - - - +
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Residues in contact with PRO 114 (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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53A TYR* 4.3 12.9 - - + -
57A TYR* 4.1 24.7 - - + -
112A GLY 3.3 2.2 - - - +
113A HIS* 1.3 101.9 - - + +
115A SER* 1.3 57.6 + - - +
116A TRP 3.5 0.5 + - - -
117A LYS* 4.0 9.4 + - - +
118A TYR 4.3 3.3 + - - -
57B TYR* 3.3 33.2 - - + +
114B PRO* 3.8 22.7 - - + -
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Residues in contact with SER 115 (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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53A TYR* 2.9 31.9 + - - -
54A MET* 4.2 13.0 - - - -
57A TYR* 3.5 14.2 - - - -
58A PHE* 4.6 0.9 - - - -
109A LEU* 3.9 8.3 - - - -
113A HIS* 3.1 21.1 + - - -
114A PRO* 1.3 75.8 - - - +
116A TRP* 1.3 65.5 + - - +
117A LYS 3.3 1.1 - - - -
118A TYR* 3.4 7.0 + - - +
119A LEU* 3.0 28.9 + - - +
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Residues in contact with TRP 116 (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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106A GLN* 3.3 45.9 + - + +
109A LEU* 3.2 31.1 - - + +
110A LEU 3.3 15.5 - - - +
111A GLU* 3.3 39.9 - - + +
113A HIS* 2.9 20.4 + - + +
115A SER* 1.3 79.9 - - - +
117A LYS* 1.3 62.2 + - - +
119A LEU* 3.5 1.9 + - - +
120A GLN* 3.2 16.3 + - - +
99H GLY 3.7 22.0 - - - -
100H SER* 3.7 35.2 - + - -
91L SER 4.0 6.3 - - - -
92L PHE* 3.3 44.8 + + - -
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Residues in contact with LYS 117 (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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113A HIS 4.2 0.8 + - - +
114A PRO 4.0 8.0 + - - +
115A SER 3.3 0.4 - - - -
116A TRP* 1.3 77.3 - - + +
118A TYR* 1.3 67.9 + - - +
120A GLN* 3.1 3.9 + - + +
121A GLU* 2.9 62.2 + - + +
28L ASP* 4.5 19.2 + - - -
30L SER* 5.5 5.9 - - - -
92L PHE* 3.9 32.5 - - + -
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Residues in contact with TYR 118 (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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44A LYS* 2.8 56.3 + - + -
45A LEU* 3.9 13.3 - - - +
49A SER* 3.6 13.2 - - - -
50A ARG* 4.2 4.9 + - - +
53A TYR* 3.3 67.1 - + + -
54A MET* 4.3 11.7 - - + -
114A PRO 4.3 1.6 + - - +
115A SER* 3.4 9.3 + - - +
116A TRP 3.4 0.4 - - - -
117A LYS* 1.3 76.5 - - - +
119A LEU* 1.3 61.4 + - + +
121A GLU* 3.1 14.2 + - - +
122A VAL* 2.8 45.3 + - + +
165A LEU* 4.2 15.3 - - + -
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Residues in contact with LEU 119 (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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54A MET* 4.1 24.2 - - + -
102A THR* 4.1 26.4 - - + +
105A VAL* 3.9 16.6 - - + -
106A GLN* 3.6 40.4 - - + +
109A LEU* 3.8 16.6 - - + -
115A SER* 3.0 27.7 + - - +
116A TRP 3.8 2.9 - - - +
118A TYR* 1.3 76.4 - - + +
120A GLN* 1.3 53.9 + - - +
122A VAL* 3.2 7.5 + - + +
123A GLU* 2.8 37.4 + - - +
165A LEU* 4.7 11.0 - - + -
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Residues in contact with GLN 120 (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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106A GLN* 3.0 19.9 + - - +
116A TRP 3.2 10.1 + - - +
117A LYS 3.1 9.7 + - - +
119A LEU* 1.3 79.0 - - - +
121A GLU* 1.3 64.0 + - + +
123A GLU* 3.1 16.0 + - - +
124A THR* 2.9 26.0 + - - +
100H SER* 3.0 29.0 + - - -
30L SER* 3.2 23.5 + - - +
31L THR* 3.0 32.2 - - + +
32L ALA* 4.2 7.5 - - - +
92L PHE* 3.7 19.5 - - + -
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Residues in contact with GLU 121 (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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44A LYS* 3.5 32.9 + - + -
117A LYS* 2.9 55.3 + - + +
118A TYR* 3.4 13.4 - - - +
120A GLN* 1.3 77.0 - - + +
122A VAL* 1.3 66.3 + - - +
124A THR* 3.4 9.1 + - - -
125A LEU* 3.2 25.9 + - + +
30L SER* 5.4 3.8 - - - +
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Residues in contact with VAL 122 (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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41A LEU* 4.6 8.5 - - + -
44A LYS* 4.5 8.0 - - + +
45A LEU* 4.6 18.4 - - + -
102A THR* 3.8 21.5 - - + -
118A TYR* 2.8 55.1 + - + +
119A LEU* 3.3 10.3 - - + +
121A GLU* 1.3 71.1 - - - +
123A GLU* 1.3 56.3 + - - +
125A LEU* 2.8 34.1 + - - +
126A LEU* 3.0 22.0 + - + +
165A LEU* 4.9 7.0 - - + -
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Residues in contact with GLU 123 (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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99A LEU* 3.9 14.3 - - + +
102A THR* 3.4 19.9 + - - +
103A GLU* 3.8 17.1 + - - +
106A GLN* 3.8 15.2 - - - +
119A LEU 2.8 19.4 + - - +
120A GLN* 3.3 20.4 + - - +
122A VAL* 1.3 75.6 - - - +
124A THR* 1.3 64.1 + - - +
126A LEU* 3.2 12.2 + - - +
127A LEU* 2.8 35.5 + - + +
100H LYS* 3.8 29.0 + - - -
31L THR* 5.7 0.9 - - - +
50L SER* 5.7 0.7 + - - -
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Residues in contact with THR 124 (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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120A GLN* 2.9 22.7 + - - +
121A GLU* 3.5 11.5 - - - -
122A VAL 3.1 0.2 + - - -
123A GLU* 1.3 71.8 - - - +
125A LEU* 1.3 63.3 + - + +
127A LEU* 3.0 14.5 + - + +
128A ASN* 2.9 40.9 + - - +
30L SER* 4.8 2.3 + - - -
31L THR* 4.2 26.0 - - + +
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Residues in contact with LEU 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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37A VAL* 4.7 2.6 - - + +
40A PHE* 4.2 23.1 - - + +
41A LEU* 3.0 31.0 - - + +
44A LYS* 4.0 34.5 - - + -
121A GLU* 3.6 13.9 - - + +
122A VAL* 2.8 13.2 + - - +
124A THR* 1.3 78.7 - - + +
126A LEU* 1.3 60.7 + - - +
128A ASN* 3.4 18.1 + - + +
129A VAL* 3.2 25.6 + - - +
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Residues in contact with LEU 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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41A LEU* 4.0 15.2 - - + +
94A TRP* 4.0 23.8 - - + -
95A VAL* 3.5 14.9 - - + +
98A SER* 3.7 31.4 - - - +
99A LEU* 3.7 20.2 - - + +
102A THR* 3.6 30.1 - - + -
122A VAL* 3.0 18.8 + - + +
123A GLU* 3.5 8.1 - - - +
125A LEU* 1.3 75.5 - - - +
127A LEU* 1.3 64.5 + - - +
129A VAL* 3.1 18.3 + - + +
130A GLN 3.1 8.8 + - - -
168A CYS* 4.3 9.6 - - - -
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Residues in contact with LEU 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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99A LEU* 4.0 17.5 - - + +
123A GLU* 2.8 34.3 + - + +
124A THR* 3.0 15.0 + - + +
126A LEU* 1.3 72.5 - - - +
128A ASN* 1.3 67.5 + - - +
130A GLN* 2.8 42.5 + - - +
131A GLN 3.6 1.7 + - - -
100H LYS* 5.8 8.7 - - - +
31L THR* 6.1 4.7 - - + -
50L SER* 5.9 1.8 - - - +
53L PHE* 3.7 41.5 - - + -
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Residues in contact with ASN 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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37A VAL* 4.5 11.9 - - + -
124A THR* 2.9 27.8 + - - +
125A LEU* 3.5 23.2 - - + +
126A LEU 3.3 0.2 - - - -
127A LEU* 1.3 75.4 - - - +
129A VAL* 1.3 54.3 + - - +
131A GLN* 2.7 39.0 + - - +
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Residues in contact with VAL 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 VAL* 3.3 28.5 - - + +
38A THR* 4.2 22.9 - - + +
41A LEU* 4.4 10.8 - - + -
94A TRP* 4.1 25.1 - - + -
95A VAL* 4.4 5.6 - - + -
125A LEU 3.2 12.5 + - - +
126A LEU* 3.1 11.6 + - - +
128A ASN* 1.3 77.5 - - - +
130A GLN* 1.3 58.0 + - - +
131A GLN 2.9 5.2 + - - -
132A GLY 3.6 2.9 + - - -
133A LEU* 3.1 23.1 - - + +
176A TYR* 4.5 9.4 - - - +
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Residues in contact with GLN 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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92A TYR* 4.4 16.0 + - + -
95A VAL* 4.2 19.7 - - + -
96A LEU* 4.1 20.6 - - - +
99A LEU* 4.1 7.3 - - + +
126A LEU 3.1 7.5 + - - +
127A LEU* 2.8 41.0 + - - +
129A VAL* 1.3 71.1 - - - +
131A GLN* 1.3 62.8 + - - +
132A GLY 3.5 0.2 - - - -
133A LEU* 3.5 15.2 + - + -
134A THR* 3.4 34.0 + - + +
53L PHE* 6.0 0.2 - - - -
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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