Contacts of the helix formed by residues 101 - 114 (chain A) in PDB entry 3FIE
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 ASN 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ILE 3.5 1.9 + - - +
99A ASN 3.2 0.6 - - - -
100A SER* 1.3 82.0 + - - +
102A PRO* 1.3 68.5 - - - +
103A ALA* 2.9 36.7 + - - +
104A GLY 3.0 4.0 + - - -
105A GLU* 2.8 29.3 + - - +
359A LYS* 3.1 30.0 + - - +
360A PHE* 3.3 37.3 - - + +
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Residues in contact with PRO 102 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A SER 4.3 4.0 - - - +
101A ASN* 1.3 91.8 - - - +
103A ALA* 1.3 57.7 + - - +
105A GLU* 3.4 18.2 + - + +
106A VAL* 3.0 31.2 + - - +
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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
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101A ASN* 2.9 17.1 + - - +
102A PRO* 1.3 72.9 - - - +
104A GLY* 1.3 65.1 + - - +
106A VAL* 3.5 8.7 + - - +
107A LEU* 3.4 17.0 + - - +
351A PHE* 4.0 7.1 - - - -
356A LEU* 3.8 18.7 - - + +
359A LYS* 3.5 33.0 - - + -
360A PHE* 5.0 0.2 - - + -
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Residues in contact with GLY 104 (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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98A ILE* 3.1 38.5 - - - +
101A ASN* 3.0 6.1 + - - -
103A ALA* 1.3 77.6 - - - +
105A GLU* 1.3 65.2 + - - +
107A LEU* 3.1 7.7 + - - +
108A LEU* 3.1 21.0 + - - +
356A LEU* 4.5 5.2 - - - -
360A PHE* 4.1 9.8 - - - -
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Residues in contact with GLU 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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2A PRO* 3.6 35.0 - - + +
3A VAL* 5.2 0.6 - - - +
98A ILE 3.4 1.3 + - - -
99A ASN* 3.4 37.2 - - - +
100A SER 5.7 0.3 - - - -
101A ASN 2.8 14.0 + - - +
102A PRO* 3.4 20.9 - - - +
104A GLY* 1.3 79.4 - - - +
106A VAL* 1.3 61.3 + - + +
108A LEU* 3.6 3.1 + - - +
109A GLN* 3.2 33.9 + - - +
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Residues in contact with VAL 106 (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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102A PRO 3.0 17.9 - - - +
103A ALA* 3.7 8.7 - - - +
104A GLY 3.2 0.6 - - - -
105A GLU* 1.3 76.9 - - + +
107A LEU* 1.3 65.5 + - - +
109A GLN* 3.2 18.2 + - - +
110A GLU* 3.0 33.1 + - + +
347A LYS* 6.2 1.1 - - + -
351A PHE* 3.9 17.7 - - + -
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Residues in contact with LEU 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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98A ILE* 4.6 6.5 - - + -
103A ALA 3.4 6.2 + - - +
104A GLY* 3.1 10.0 + - - +
106A VAL* 1.3 80.4 - - - +
108A LEU* 1.3 57.2 + - - +
110A GLU* 3.4 1.4 + - - +
111A ILE* 2.9 49.5 + - + +
226A ALA* 3.9 38.6 - - + +
229A LEU* 4.2 11.4 - - + -
230A ILE* 4.2 13.5 - - + +
233A LEU* 4.4 7.6 - - + -
351A PHE* 3.5 40.5 - - + -
356A LEU* 4.2 13.5 - - + -
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A VAL* 3.9 18.4 - - + -
5A ILE* 4.7 2.9 - - + -
40A MET* 3.2 20.5 - - - +
95A PHE* 3.6 42.2 - - + +
98A ILE* 4.0 7.9 - - + -
99A ASN* 3.5 42.4 - - + +
104A GLY 3.1 14.5 + - - +
105A GLU 4.0 2.9 - - - +
106A VAL 3.3 0.2 - - - -
107A LEU* 1.3 73.4 - - - +
109A GLN* 1.3 65.2 + - - +
111A ILE* 3.4 5.6 + - + +
112A SER 2.9 18.5 + - - -
229A LEU* 3.7 23.6 - - + -
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Residues in contact with GLN 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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2A PRO* 3.0 32.2 - - - +
3A VAL* 3.8 20.6 - - + +
105A GLU* 3.2 26.1 + - - +
106A VAL* 3.2 27.7 + - - +
108A LEU* 1.3 74.4 - - - +
110A GLU* 1.3 60.5 - - + +
112A SER* 3.0 3.5 + - - -
113A TYR* 2.9 64.0 + - + +
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Residues in contact with GLU 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 VAL* 3.0 28.3 + - + +
107A LEU 3.6 4.9 - - - +
109A GLN* 1.3 78.7 - - - +
111A ILE* 1.3 56.0 + - - +
113A TYR* 3.3 11.1 + - - +
114A ALA* 2.9 32.9 + - - +
233A LEU* 3.7 20.7 - - + +
237A TYR* 4.1 5.9 + - - -
322A TRP* 4.7 1.6 - - - -
347A LYS* 3.1 42.0 + - + +
351A PHE* 3.9 19.3 - - + -
25C ASN* 3.3 25.6 + - - -
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Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A MET* 4.9 3.1 - - + -
43A VAL* 3.8 25.1 - - + +
95A PHE* 6.0 0.4 - - + -
107A LEU* 2.9 31.1 + - + +
108A LEU* 3.6 10.3 - - + +
110A GLU* 1.3 77.0 - - - +
112A SER* 1.3 61.7 + - - +
114A ALA* 3.6 6.6 + - - +
152A ASN* 3.2 18.5 + - - +
153A LEU* 4.1 15.5 - - + -
229A LEU* 3.2 45.3 - - + +
232A ALA* 4.4 6.1 - - + -
233A LEU* 3.8 24.0 - - + +
236A LEU* 4.4 5.2 - - + +
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Residues in contact with SER 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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3A VAL* 4.3 8.6 - - - +
40A MET* 3.2 25.3 - - - +
41A ARG* 3.0 36.2 + - - +
42A ASN* 2.8 26.4 - - - +
43A VAL* 5.1 0.4 - - - -
108A LEU 2.9 6.7 + - - -
109A GLN 3.0 8.0 + - - -
111A ILE* 1.3 78.6 - - - +
113A TYR* 1.3 65.6 + - - +
152A ASN* 2.9 7.7 + - - +
319A TYR* 4.5 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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2A PRO 5.4 0.5 - - - -
3A VAL* 5.4 3.8 - - + +
109A GLN* 2.9 60.7 + - + +
110A GLU* 4.1 12.6 - - - +
112A SER* 1.3 82.7 - - - +
114A ALA* 1.3 51.6 + - - +
115A LYS 2.7 17.6 + - - -
319A TYR* 2.7 34.7 + - - +
322A TRP* 3.6 18.7 - + + -
323A LYS* 5.4 0.2 - - - +
25C ASN* 3.8 28.9 - - + -
26C LEU* 3.4 32.2 - - + +
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Residues in contact with ALA 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 GLU 2.9 17.9 + - - +
111A ILE 3.8 7.9 - - - +
112A SER 3.3 2.0 - - - -
113A TYR* 1.3 74.0 - - - +
115A LYS* 1.3 62.1 + - - +
116A PRO* 3.5 4.3 - - - +
152A ASN* 3.5 14.6 - - - -
233A LEU* 4.0 4.5 - - + -
236A LEU* 3.6 30.1 - - + +
237A TYR* 3.7 29.6 - - + -
323A LYS* 4.6 2.9 - - - +
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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