Contacts of the helix formed by residues 117 - 136 (chain A) in PDB entry 4IKV
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 GLY 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A TYR* 4.7 2.6 + - - -
59A LEU* 3.8 21.4 - - - +
116A GLY* 1.3 74.0 - - - -
118A VAL* 1.3 65.3 + - - -
119A ALA* 3.4 2.9 - - - +
120A ALA* 3.3 9.2 + - - +
121A LEU* 3.3 16.3 + - - +
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Residues in contact with VAL 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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59A LEU* 3.9 25.4 - - + +
61A LEU* 3.9 28.0 - - + -
117A GLY* 1.3 69.6 - - - -
119A ALA* 1.3 65.3 + - - +
121A LEU* 3.1 23.0 + - + +
122A PHE* 3.2 13.4 + - + +
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLY 3.4 0.8 - - - -
118A VAL* 1.3 78.7 - - - +
120A ALA* 1.3 57.9 + - - +
122A PHE* 3.3 10.8 + - - +
123A VAL* 3.0 32.4 + - + +
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Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 6.0 0.7 - - - +
111A ALA* 3.6 25.7 - - + +
112A LEU* 4.5 5.4 - - + -
114A ILE* 5.9 1.6 - - + -
116A GLY* 4.5 8.5 - - - -
117A GLY 3.3 22.0 + - - +
118A VAL 3.2 0.6 - - - -
119A ALA* 1.3 75.1 - - - +
121A LEU* 1.3 62.1 + - - +
123A VAL* 3.8 8.0 - - - +
124A SER* 2.8 31.5 + - - -
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Residues in contact with LEU 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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46A LEU* 4.1 25.1 - - + -
50A MET* 3.7 28.9 - - + -
59A LEU* 3.8 21.3 - - + -
61A LEU* 4.5 6.3 - - + -
69A ILE* 4.5 13.7 - - + -
112A LEU* 4.1 14.5 - - + +
117A GLY 3.3 11.0 + - - +
118A VAL* 3.1 16.3 + - + +
120A ALA* 1.3 76.5 - - - +
122A PHE* 1.3 63.5 + - - +
124A SER* 3.3 1.7 + - - -
125A MET* 3.0 45.6 + - + +
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Residues in contact with PHE 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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118A VAL* 3.2 9.1 + - + +
119A ALA* 3.4 13.2 - - - +
121A LEU* 1.3 81.1 - - - +
123A VAL* 1.3 60.2 + - + +
125A MET* 3.4 7.7 + - + +
126A ALA* 2.9 36.1 + - + +
254A PHE* 6.2 6.7 - + - -
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Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ALA* 4.5 8.7 - - + -
119A ALA* 3.0 21.8 + - + +
120A ALA* 3.9 7.4 - - - +
122A PHE* 1.3 76.9 - - + +
124A SER* 1.3 63.0 + - - +
126A ALA* 3.3 7.2 + - + +
127A LEU* 2.9 44.1 + - + +
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Residues in contact with SER 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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73A TYR* 4.8 1.0 + - - -
108A GLY* 2.9 31.0 + - - -
111A ALA* 4.1 4.5 - - - +
112A LEU* 3.3 30.2 - - - +
120A ALA 2.8 19.8 + - - -
121A LEU 3.6 4.3 - - - -
123A VAL* 1.3 76.8 - - - +
125A MET* 1.3 58.9 + - - +
127A LEU* 3.4 0.9 + - - +
128A ILE* 2.9 41.5 + - - +
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Residues in contact with MET 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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46A LEU* 5.1 0.7 - - + -
69A ILE* 3.5 36.1 - - + +
72A ILE* 5.1 3.6 - - + -
73A TYR* 3.7 50.3 - - + +
76A LEU* 4.4 20.9 - - + -
121A LEU* 3.0 39.6 + - + +
122A PHE* 3.8 8.1 - - + +
124A SER* 1.3 73.0 - - - +
126A ALA* 1.3 60.6 + - - +
129A VAL* 2.8 37.9 + - + +
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Residues in contact with ALA 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 PHE* 2.9 26.4 + - + +
123A VAL* 3.5 11.0 - - + +
125A MET* 1.3 76.5 - - - +
127A LEU* 1.3 64.6 + - + +
129A VAL* 3.9 3.3 - - - +
130A LEU* 3.0 38.0 + - + +
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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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104A LEU* 3.4 43.3 - - + +
107A ALA* 3.9 17.3 - - + +
108A GLY* 3.8 22.7 - - - +
111A ALA* 4.9 1.6 - - + -
123A VAL* 2.9 39.3 + - + +
126A ALA* 1.3 77.4 - - + +
128A ILE* 1.3 59.2 + - - +
130A LEU* 3.8 8.9 - - + +
131A GLY* 2.9 28.2 + - - -
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Residues in contact with ILE 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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39A TYR* 4.3 15.9 - - + -
42A MET* 4.1 7.6 - - + -
73A TYR* 3.3 34.5 - - + +
105A ILE* 3.9 21.8 - - + +
108A GLY* 3.9 15.0 - - - -
109A HIS* 3.8 30.7 - - + +
124A SER* 2.9 30.5 + - - +
127A LEU* 1.3 72.0 - - - +
129A VAL* 1.3 61.8 + - - +
132A THR* 2.7 48.0 + - - +
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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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73A TYR* 3.9 20.9 - - + -
76A LEU* 3.7 42.2 - - + +
77A VAL* 4.4 9.2 - - + -
80A SER* 2.7 38.7 + - - -
125A MET* 2.8 29.4 + - + +
126A ALA* 3.9 4.0 - - - +
128A ILE* 1.3 72.0 - - - +
130A LEU* 1.3 63.1 + - + +
132A THR* 4.2 0.7 - - - -
133A GLY 3.1 13.0 + - - -
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Residues in contact with LEU 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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80A SER* 3.7 11.5 + - - +
104A LEU* 4.4 16.4 - - + -
126A ALA* 3.0 29.3 + - + +
127A LEU* 3.8 10.8 - - + +
129A VAL* 1.3 83.5 - - + +
131A GLY* 1.3 62.6 + - - +
133A GLY 3.4 0.7 + - - -
134A LEU* 3.3 25.1 + - + +
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Residues in contact with GLY 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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101A GLY* 3.3 29.9 - - - -
104A LEU* 3.7 10.9 - - - +
105A ILE* 3.6 8.3 - - - -
127A LEU 2.9 22.0 + - - -
130A LEU* 1.3 73.4 - - - +
132A THR* 1.3 56.9 + - - +
134A LEU 3.1 2.3 + - - -
135A LEU* 3.0 24.4 + - - +
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Residues in contact with THR 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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35A GLU* 3.9 16.6 + - - +
36A ARG* 4.0 9.9 - - - +
39A TYR* 4.8 4.6 - - + -
77A VAL* 3.8 29.2 - - + -
105A ILE* 3.6 16.9 - - - +
128A ILE* 2.7 41.6 + - - +
129A VAL 4.2 1.8 - - - -
131A GLY* 1.3 71.6 - - - +
133A GLY* 1.3 57.2 + - - +
135A LEU 4.4 0.4 - - - +
136A LYS* 2.8 51.7 + - + +
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Residues in contact with GLY 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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77A VAL* 4.5 2.8 + - - -
80A SER* 3.3 21.5 - - - -
81A GLY* 3.6 18.0 - - - -
84A GLY* 3.2 21.4 - - - -
129A VAL 3.1 11.1 + - - -
130A LEU 3.8 0.9 - - - -
131A GLY 3.2 0.2 - - - -
132A THR* 1.3 78.7 - - - +
134A LEU* 1.3 55.5 + - - +
137A PRO* 3.1 19.1 - - - +
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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
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84A GLY* 4.1 11.9 - - - +
87A LEU* 3.7 32.8 - - + -
92A PHE* 4.1 21.3 - - + -
97A ALA* 3.4 26.2 - - + +
100A TYR* 4.6 9.2 - - + -
101A GLY* 3.9 9.9 - - - +
104A LEU* 4.1 22.2 - - + -
130A LEU* 3.3 15.5 + - + +
131A GLY 3.1 7.6 + - - +
133A GLY* 1.3 76.9 - - - +
135A LEU* 1.3 62.1 + - - +
138A ASN* 2.8 27.3 + - - +
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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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31A THR* 4.7 7.2 - - + -
32A GLU* 4.2 8.3 - - - +
35A GLU* 4.0 34.5 - - + +
98A VAL* 3.6 41.7 - - + +
101A GLY* 4.4 1.6 - - - -
102A GLY* 3.9 15.7 - - - +
105A ILE* 4.0 6.3 - - + -
131A GLY 3.0 15.2 + - - +
132A THR 4.3 0.2 - - - +
134A LEU* 1.3 78.7 - - - +
136A LYS* 1.3 72.8 + - - +
137A PRO 3.5 0.2 - - - -
138A ASN 3.2 1.4 + - - -
139A VAL* 3.1 43.9 + - + +
196A MET* 4.4 8.5 - - + -
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Residues in contact with LYS 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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32A GLU* 5.6 4.9 - - - +
35A GLU* 5.2 2.2 - - - +
36A ARG* 3.5 37.1 - - - +
39A TYR* 5.9 2.2 - - - -
77A VAL* 4.3 19.0 - - + +
132A THR* 2.8 39.5 + - + +
135A LEU* 1.3 82.8 - - + +
137A PRO* 1.3 64.0 - - + +
138A ASN 3.2 1.0 + - - -
139A VAL* 3.7 13.1 - - - +
140A SER* 4.9 3.3 + - - -
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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
------------------------------------------------------------
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