Contacts of the helix formed by residues 101 - 118 (chain A) in PDB entry 4M8J
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 101 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A THR* 1.3 77.5 - - - +
102A ALA* 1.3 61.7 + - - +
103A ALA* 3.3 7.4 + - - +
104A VAL* 3.1 38.3 + - - +
105A LEU* 3.4 17.7 - - - +
414A LEU* 5.0 1.6 - - - +
418A ALA* 4.1 18.9 - - - +
422A LEU* 5.0 11.9 - - - -
601A NM2 3.9 27.1 - - - +
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Residues in contact with ALA 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A SER* 1.3 74.8 - - - +
103A ALA* 1.3 65.9 + - - +
104A VAL 3.1 2.8 + - - -
105A LEU* 3.4 9.3 + - - +
106A PHE 3.3 7.1 + - - -
207A SER 5.0 1.3 - - - +
211A ALA* 3.7 33.9 - - + -
214A LEU* 3.2 22.3 - - - +
415A CYS* 4.3 11.0 - - - +
418A ALA* 4.2 5.4 + - + +
419A THR* 3.8 17.3 - - + -
422A LEU* 5.6 4.8 - - + +
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A SER* 3.3 5.9 + - - +
102A ALA* 1.3 80.3 - - - +
104A VAL* 1.3 57.0 + - - +
106A PHE* 3.3 8.8 - - - +
107A TRP* 2.9 37.9 + - + -
207A SER* 5.2 11.6 + - - +
210A LEU* 3.7 30.9 - - + +
323A TRP* 4.3 22.2 - - + -
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A CYS 3.9 10.1 - - - +
100A THR* 4.2 1.3 - - - -
101A SER* 3.1 44.1 + - - +
103A ALA* 1.3 74.7 - - - +
105A LEU* 1.3 62.6 + - + +
106A PHE 3.0 1.8 - - - -
107A TRP* 4.3 1.1 - - - +
108A GLY* 2.5 34.8 + - - -
323A TRP* 5.9 1.7 - - + -
362A ILE* 3.6 28.4 - - + +
363A TRP* 3.4 37.5 - - + -
601A NM2 5.4 6.1 - - + -
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Residues in contact with LEU 105 (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 SER 3.4 20.4 - - - +
102A ALA* 3.4 8.0 + - - +
104A VAL* 1.3 80.6 - - + +
106A PHE* 1.3 57.2 + - - +
109A SER* 2.4 32.9 + - - -
214A LEU* 5.0 1.3 - - + -
266A SER* 6.1 0.7 - - - +
270A LEU* 5.7 4.7 - - + -
362A ILE* 5.8 1.3 - - + -
366A LEU* 4.0 19.7 - - + -
398A TRP* 3.9 18.0 - - + -
411A PHE* 3.8 32.5 - - + -
414A LEU* 4.3 26.7 - - + -
415A CYS* 4.2 26.2 - - + +
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Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ALA 3.3 11.6 + - - +
103A ALA* 3.3 12.1 - - - +
105A LEU* 1.3 81.0 - - - +
107A TRP* 1.3 102.7 + + - +
110A ILE* 3.4 14.1 + - + +
210A LEU* 3.9 28.3 - - + +
213A PRO* 5.3 0.2 - - + -
214A LEU* 3.6 23.3 - - + +
390A VAL* 3.7 22.4 - - + -
391A PRO* 4.0 24.0 - - + -
394A ILE* 3.2 38.2 - - + +
469A LEU* 3.8 18.2 - - + -
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Residues in contact with TRP 107 (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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103A ALA* 2.9 32.4 + - + +
104A VAL* 5.0 0.2 - - - -
106A PHE* 1.3 100.8 - + - +
108A GLY* 1.3 62.6 + - - +
109A SER 3.0 6.8 + - - -
110A ILE* 4.3 11.9 - - + +
111A GLU* 3.0 35.9 + - + +
142A TRP* 4.8 13.9 - + + -
210A LEU* 3.6 26.0 - - + +
316A TRP* 3.7 31.2 - + - -
319A PHE* 3.8 25.8 - + - -
320A TYR* 3.7 17.9 - + - -
323A TRP* 5.2 10.4 - + - -
363A TRP* 3.7 20.1 + + + +
469A LEU* 4.2 20.4 - - + -
472A ILE* 5.1 3.6 - - + -
473A GLN* 5.5 2.5 - - + -
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Residues in contact with GLY 108 (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 VAL 2.5 23.1 + - - -
107A TRP* 1.3 72.2 - - - +
109A SER* 1.3 56.6 + - - +
111A GLU* 4.9 0.4 - - - -
112A ILE 5.7 0.3 + - - -
362A ILE* 4.7 1.1 - - - -
363A TRP* 3.9 28.6 - - - +
366A LEU* 3.2 15.3 - - - +
367A GLY* 3.0 31.0 + - - -
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Residues in contact with SER 109 (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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105A LEU 2.4 26.1 + - - -
106A PHE 3.5 1.3 + - - -
107A TRP 3.0 0.8 - - - -
108A GLY* 1.3 81.0 - - - +
110A ILE* 1.3 61.3 + - - +
111A GLU 3.6 0.7 - - - -
112A ILE* 4.2 3.5 - - - +
366A LEU* 4.0 10.4 - - - +
370A THR* 2.7 41.4 + - - +
394A ILE* 3.6 23.3 - - - +
397A THR* 4.6 4.4 - - - +
398A TRP* 3.5 19.5 + - - -
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Residues in contact with ILE 110 (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 PHE* 3.4 14.7 + - + +
107A TRP* 4.3 17.7 - - + -
109A SER* 1.3 79.1 - - - +
111A GLU* 1.3 68.3 + - - +
112A ILE 3.2 3.1 - - - -
113A TYR* 3.1 23.5 + - + +
114A TYR* 3.3 35.2 - - + -
370A THR* 5.1 2.7 - - + -
381A ILE* 3.8 33.4 - - + -
385A ILE* 4.6 1.6 - - + -
390A VAL* 4.1 16.6 - - + -
393A ALA* 4.6 8.3 - - + -
394A ILE* 3.9 24.9 - - + +
397A THR* 5.7 1.6 - - + -
469A LEU* 5.9 0.2 - - + -
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Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TRP* 3.0 23.3 + - + +
108A GLY 5.4 0.2 - - - -
109A SER 3.6 0.2 - - - -
110A ILE* 1.3 82.1 - - - +
112A ILE* 1.3 63.4 + - - +
114A TYR* 3.2 16.3 + - - +
115A TYR* 3.1 40.2 + - + +
138A SER* 2.3 40.3 + - - +
142A TRP* 2.6 25.3 + - - -
316A TRP* 5.0 2.9 - - + -
320A TYR* 2.6 28.2 + - - +
363A TRP* 3.2 11.4 + - + +
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Residues in contact with ILE 112 (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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108A GLY 5.7 0.4 + - - -
109A SER 4.2 2.7 - - - +
111A GLU* 1.3 74.9 - - - +
113A TYR* 1.3 64.1 + - - +
115A TYR* 3.3 9.6 + - - +
116A ILE* 3.0 28.6 + - + +
134A GLY* 4.3 17.0 - - - +
135A LEU* 4.3 9.6 - - + +
138A SER* 5.0 4.2 + - - +
285A TYR* 4.1 15.9 - - + +
367A GLY* 3.4 44.1 - - - +
368A GLY 4.4 0.2 - - - +
370A THR* 3.8 22.0 - - + -
371A LEU* 3.6 34.1 - - + +
374A ILE* 5.3 0.9 - - + -
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Residues in contact with TYR 113 (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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110A ILE* 3.1 20.4 + - + +
112A ILE* 1.3 82.0 - - - +
114A TYR* 1.3 89.0 + + - +
116A ILE* 3.1 8.4 - - + +
117A SER* 2.8 38.6 + - - -
126A TYR* 3.5 25.1 - - - -
370A THR* 4.9 2.9 - - + -
374A ILE* 4.1 20.2 - - + -
381A ILE* 3.9 24.9 - - + -
382A PRO* 3.5 30.2 - - + +
385A ILE* 3.7 21.3 - - + +
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Residues in contact with TYR 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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110A ILE* 3.3 46.4 + - + -
111A GLU* 3.2 7.0 + - - +
113A TYR* 1.3 98.5 - + - +
115A TYR* 1.3 65.4 + - + +
117A SER* 3.5 14.2 + - - -
118A SER* 3.4 18.4 + - - +
312A PHE* 4.7 0.5 - - - -
316A TRP* 3.4 50.0 + + + +
385A ILE* 3.6 20.9 - - + +
390A VAL* 3.9 16.1 - - - +
469A LEU* 4.2 13.2 - - + +
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Residues in contact with TYR 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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111A GLU* 3.1 52.7 + - + -
112A ILE* 3.7 7.4 - - - +
114A TYR* 1.3 80.3 - - - +
116A ILE* 1.3 59.5 + - - +
119A PRO* 3.3 27.3 - - - +
120A PRO* 4.2 4.3 - - + +
130A ALA 4.2 6.4 - - - +
133A ILE* 5.1 0.8 - - + +
134A GLY* 3.2 32.3 - - - +
137A TYR* 3.8 17.3 - + + -
138A SER* 3.4 8.5 - - - -
141A HIS* 2.8 29.1 + + - -
312A PHE* 3.6 35.0 - + + -
316A TRP* 3.9 19.7 - + + -
320A TYR* 3.2 7.1 - - - -
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Residues in contact with ILE 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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112A ILE* 3.0 20.4 + - + +
113A TYR* 3.1 24.5 - - + +
115A TYR* 1.3 78.6 - - - +
117A SER* 1.3 66.4 + - - +
119A PRO* 4.2 3.5 - - - +
126A TYR* 3.1 40.5 + - + -
127A SER 4.0 1.6 - - - +
130A ALA* 3.3 13.9 - - + +
131A LYS* 3.3 59.2 - - + +
134A GLY* 5.8 1.3 - - - -
371A LEU* 5.3 6.3 - - + -
374A ILE* 4.3 17.0 - - + -
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Residues in contact with SER 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A TYR* 2.8 44.1 + - - -
114A TYR* 3.5 16.1 + - - -
116A ILE* 1.3 77.1 - - - +
118A SER* 1.3 76.4 + - - +
119A PRO* 3.1 8.1 - - - +
125A GLY* 3.2 16.3 - - - -
126A TYR* 4.1 19.4 - - - -
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Residues in contact with SER 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TYR 3.4 15.1 + - - +
115A TYR 4.3 0.2 - - - -
117A SER* 1.3 90.7 + - - +
119A PRO* 1.3 68.0 + - - +
312A PHE* 3.8 10.9 - - - -
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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
------------------------------------------------------------
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