Contacts of the helix formed by residues 113 - 128 (chain A) in PDB entry 1EKF
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 ASP 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A SER* 3.9 13.4 - - - -
5A PHE* 4.9 1.9 + - - +
6A LYS* 6.0 1.6 - - - +
112A PHE* 1.3 79.1 - - - +
114A LYS* 1.3 63.7 + - - +
115A LEU* 2.9 35.9 + - - +
116A GLU* 3.2 34.9 + - + +
117A LEU 3.0 17.7 + - - -
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Residues in contact with LYS 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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97A MET* 3.4 47.2 - - + +
98A ASP* 2.4 38.3 + - - +
101A LEU* 4.0 27.9 - - + +
112A PHE* 3.5 17.2 + - + -
113A ASP* 1.3 73.5 + - - +
115A LEU* 1.3 63.1 + - + +
117A LEU* 3.9 0.9 - - - +
118A LEU* 3.0 27.4 + - - +
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Residues in contact with LEU 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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94A TRP* 4.2 26.9 - - + +
113A ASP* 2.9 10.7 + - - +
114A LYS* 1.3 79.8 - - + +
116A GLU* 1.3 66.8 + - + +
118A LEU* 3.8 10.1 - - + +
119A GLU* 3.0 23.6 + - - +
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Residues in contact with GLU 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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5A PHE* 3.3 27.8 - - + +
6A LYS* 3.4 18.5 + - + +
7A ALA* 3.0 29.7 + - - +
8A ALA 4.9 0.2 + - - -
113A ASP* 3.1 35.1 + - + +
115A LEU* 1.3 79.7 - - - +
117A LEU* 1.3 62.0 + - - +
119A GLU* 3.3 6.0 + - - +
120A CYS* 3.1 25.6 + - - -
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Residues in contact with LEU 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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5A PHE* 4.0 20.8 - - + -
39A LEU* 3.9 25.4 - - + -
97A MET* 3.6 17.0 - - + -
100A MET* 3.7 24.7 - - + -
112A PHE* 3.6 31.6 - - + -
113A ASP 3.0 13.8 + - - +
114A LYS 3.9 4.3 - - - +
116A GLU* 1.3 75.5 - - - +
118A LEU* 1.3 67.3 + - - +
120A CYS* 3.2 2.0 + - - +
121A ILE* 2.8 36.2 + - + +
144A PRO* 5.2 0.9 - - + -
163A LEU* 4.2 11.7 - - + -
165A VAL* 4.7 1.1 - - + -
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Residues in contact with LEU 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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78A MET* 4.9 6.3 - - + -
90A LEU* 4.0 10.3 - - + -
93A PRO* 3.5 29.4 - - + -
94A TRP* 3.6 36.6 - - + +
97A MET* 4.1 10.9 - - + -
114A LYS 3.0 18.3 + - - +
115A LEU* 3.8 12.3 - - + +
116A GLU 3.3 0.2 - - - -
117A LEU* 1.3 75.1 - - - +
119A GLU* 1.3 52.5 + - - +
121A ILE* 3.2 5.2 + - + +
122A ARG* 2.8 33.3 + - - +
363A PHE* 3.7 36.3 - - + -
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Residues in contact with GLU 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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7A ALA* 3.6 20.5 - - + +
115A LEU 3.0 14.4 + - - +
116A GLU* 3.5 9.6 - - - +
117A LEU 3.2 0.2 - - - -
118A LEU* 1.3 76.3 - - - +
120A CYS* 1.3 58.0 + - - +
122A ARG* 2.9 52.9 + - - +
123A ARG* 2.8 48.1 + - - +
363A PHE* 5.0 4.5 - - - -
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Residues in contact with CYS 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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5A PHE* 4.2 11.4 - - - -
7A ALA* 3.9 18.6 - - - -
10A LEU* 4.0 15.3 - - + -
39A LEU* 3.7 25.6 - - + +
51A PRO* 3.8 31.2 - - - -
53A ILE* 4.4 3.1 - - - +
116A GLU 3.1 15.0 + - - -
117A LEU* 3.6 7.9 - - + +
119A GLU* 1.3 79.4 - - - +
121A ILE* 1.3 57.7 + - - +
123A ARG* 3.3 3.1 + - - +
124A LEU* 2.9 28.2 + - - +
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Residues in contact with ILE 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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39A LEU* 4.6 1.8 - - + -
78A MET* 3.8 33.7 - - + -
90A LEU* 4.2 6.5 - - + -
97A MET* 4.0 12.3 - - + -
117A LEU* 2.8 43.2 + - + +
118A LEU* 3.5 8.5 - - - +
120A CYS* 1.3 73.7 - - - +
122A ARG* 1.3 65.3 + - - +
124A LEU* 3.2 7.9 + - + +
125A ILE* 2.9 41.8 + - + +
142A VAL* 4.2 7.6 - - + -
144A PRO* 4.3 12.6 - - + -
165A VAL* 4.2 17.0 - - + -
167A LEU* 5.9 0.2 - - + -
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Residues in contact with ARG 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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90A LEU* 5.2 1.8 - - - -
118A LEU 2.8 13.1 + - - +
119A GLU* 2.9 40.5 + - - +
121A ILE* 1.3 78.3 - - - +
123A ARG* 1.3 87.2 + - - +
125A ILE* 3.3 6.8 + - - +
126A GLU* 2.9 49.0 + - - +
363A PHE* 3.9 21.5 - - + -
364A PRO 3.9 5.6 - - - -
365A VAL* 2.4 50.6 - - + +
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Residues in contact with ARG 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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7A ALA* 5.4 3.1 + - + +
10A LEU* 3.8 25.0 - - + +
12A LEU* 3.7 31.4 - - - +
53A ILE* 3.7 10.9 - - + +
119A GLU* 2.8 31.7 + - - +
120A CYS 3.5 6.7 - - - +
122A ARG* 1.3 103.8 - - - +
124A LEU* 1.3 60.3 + - - +
126A GLU* 3.3 17.5 + - - +
127A VAL* 3.0 37.9 + - - +
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Residues in contact with LEU 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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37A HIS* 3.8 17.3 - - + +
38A MET* 3.7 30.5 - - - +
39A LEU* 3.7 26.7 - - + +
53A ILE* 3.6 18.1 - - + +
120A CYS 2.9 14.0 + - - +
121A ILE* 3.2 10.3 + - - +
123A ARG* 1.3 75.1 - - - +
125A ILE* 1.3 65.5 + - - +
127A VAL* 3.2 5.1 + - - +
128A ASP* 3.0 21.4 + - - +
165A VAL* 3.8 27.8 - - + +
167A LEU* 3.8 21.5 - - + +
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Residues in contact with ILE 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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80A ALA* 4.0 5.2 - - + -
88A VAL* 4.1 24.9 - - + -
90A LEU* 3.7 41.1 - - + -
121A ILE* 2.9 25.4 + - + +
122A ARG* 3.8 4.0 - - - +
124A LEU* 1.3 73.7 - - + +
126A GLU* 1.3 55.4 + - - +
128A ASP 3.2 1.4 + - - -
129A LYS* 2.7 33.6 + - + +
132A VAL* 4.5 5.4 - - + -
140A LEU* 4.1 20.0 - - + -
142A VAL* 3.8 17.3 - - + -
167A LEU* 4.4 13.9 - - + -
365A VAL* 4.3 9.9 - - - +
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Residues in contact with GLU 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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122A ARG* 2.9 39.8 + - + +
123A ARG* 3.4 26.1 + - - +
125A ILE* 1.3 75.6 - - - +
127A VAL* 1.3 65.2 + - + +
129A LYS* 3.1 43.6 + - + +
365A VAL* 4.7 20.6 + - + +
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Residues in contact with VAL 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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12A LEU* 4.9 10.8 - - + -
14A MET* 4.1 18.1 - - + +
37A HIS* 3.7 41.0 - - + +
53A ILE* 4.2 20.9 - - + -
123A ARG* 3.0 23.5 + - - +
124A LEU* 3.2 8.3 + - - +
126A GLU* 1.3 80.6 - - + +
128A ASP* 1.3 60.8 + - - +
129A LYS* 3.6 2.3 + - - +
130A ASP* 5.1 1.7 + - - +
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Residues in contact with ASP 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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35A THR* 2.6 32.8 + - + +
36A ASP* 3.8 5.1 - - - +
37A HIS* 2.7 53.6 + - - +
124A LEU* 3.0 14.5 + - - +
125A ILE* 3.3 3.4 - - - +
127A VAL* 1.3 76.4 - - - +
129A LYS* 1.3 52.3 + - - +
130A ASP 3.1 3.4 - - - -
131A TRP* 2.8 44.3 + - + +
132A VAL* 4.1 3.2 + - - +
140A LEU* 5.5 2.0 - - + +
167A LEU* 4.2 11.9 - - + +
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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
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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