Contacts of the helix formed by residues 95 - 114 (chain F) in PDB entry 4F2N
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 95 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88F ALA 5.5 0.2 + - - -
89F THR* 3.7 30.5 - - - +
92F ILE* 3.0 25.6 + - - +
94F GLU* 1.3 78.5 + - - +
96F LYS* 1.3 58.2 + - - +
97F VAL 3.4 2.9 - - - -
98F MET* 3.4 16.4 + - - +
99F PHE* 2.8 29.9 + - - +
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Residues in contact with LYS 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E PHE* 5.6 1.8 - - - -
89F THR 5.6 0.2 - - - -
92F ILE 3.5 5.0 + - - +
93F ASN* 3.2 29.7 + - - +
94F GLU 3.6 1.0 - - - -
95F SER* 1.3 74.7 - - - +
97F VAL* 1.3 65.0 + - + +
99F PHE* 3.4 22.8 + - + -
100F ASN* 2.9 55.9 + - - +
175F ASN* 6.0 2.8 - - - +
176F ALA* 5.6 1.2 - - - +
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Residues in contact with VAL 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F LYS* 4.4 16.6 - - - -
73F LEU* 3.9 18.8 - - + -
94F GLU 5.4 0.4 + - - -
95F SER 3.4 0.6 - - - -
96F LYS* 1.3 79.1 - - + +
98F MET* 1.3 62.9 + - - +
100F ASN* 3.3 7.1 + - - +
101F GLN* 3.1 37.8 + - - +
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Residues in contact with MET 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70F LEU* 4.2 8.5 - - + +
73F LEU* 3.5 49.0 - - + +
74F GLY* 4.0 9.6 - - - -
77F TYR* 4.4 13.5 - - + +
85F ILE* 3.9 24.2 - - + -
89F THR* 3.9 19.3 - - + -
95F SER* 3.4 18.0 + - - +
97F VAL* 1.3 77.2 - - - +
99F PHE* 1.3 65.7 + - - +
101F GLN* 3.3 3.4 + - - +
102F ALA* 2.9 22.7 + - - +
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Residues in contact with PHE 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F ILE* 3.7 24.0 - - + -
89F THR* 3.5 28.2 + - - +
90F THR* 3.7 36.6 - - - -
95F SER 2.8 21.3 + - - +
96F LYS* 3.4 24.0 + - + +
98F MET* 1.3 71.5 - - - +
100F ASN* 1.3 72.1 + - - +
102F ALA* 3.9 2.0 - - - +
103F ALA* 2.7 55.8 + - + +
176F ALA* 4.3 13.5 - - + -
177F GLY* 4.7 8.3 - - - -
178F CYS 5.0 1.8 - - - -
181F THR* 4.1 8.1 - - + -
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Residues in contact with ASN 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152E PHE* 3.4 48.5 - - + +
96F LYS* 2.9 56.0 + - - +
97F VAL* 3.6 8.8 - - - +
98F MET 3.3 0.4 - - - -
99F PHE* 1.3 81.4 - - - +
101F GLN* 1.3 60.4 + - - +
104F GLN* 2.9 36.2 + - - +
176F ALA* 3.6 13.4 - - - +
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Residues in contact with GLN 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E PHE* 4.7 8.1 - - - -
65F ALA 4.2 0.5 - - - +
66F TYR* 3.2 45.3 - - - +
69F LYS* 3.3 39.9 - - + +
70F LEU* 3.9 15.0 - - + +
73F LEU* 4.4 5.2 - - + -
97F VAL* 3.1 26.8 + - + +
98F MET 3.8 4.0 - - - +
100F ASN* 1.3 80.7 - - - +
102F ALA* 1.3 62.0 + - - +
104F GLN* 4.0 0.3 - - - +
105F HIS* 2.9 31.8 + - - +
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Residues in contact with ALA 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F LEU* 3.9 18.8 - - + +
82F ILE* 3.3 14.7 - - + +
85F ILE* 3.7 29.8 - - + -
86F ILE* 3.9 14.1 - - + +
98F MET 2.9 21.4 + - - +
99F PHE* 3.9 2.9 - - - +
101F GLN* 1.3 72.7 - - - +
103F ALA* 1.3 63.9 + - - +
105F HIS* 3.4 0.3 + - - +
106F PHE* 3.0 18.9 + - - +
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Residues in contact with ALA 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F ILE* 3.7 16.9 - - + +
99F PHE* 2.7 37.0 + - + +
102F ALA* 1.3 74.0 - - - +
104F GLN* 1.3 56.2 + - - +
106F PHE* 3.3 2.4 + - - +
107F ASN* 2.8 37.9 + - - +
176F ALA* 3.3 29.2 - - + +
178F CYS* 4.6 5.2 - - + -
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Residues in contact with GLN 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E PHE* 3.9 4.3 - - + -
66F TYR* 3.1 52.7 + - + -
100F ASN 2.9 21.4 + - - +
101F GLN 4.0 0.2 - - - +
103F ALA* 1.3 75.3 - - - +
105F HIS* 1.3 63.2 + - - +
107F ASN* 3.3 7.5 + - - +
108F HIS* 2.8 47.1 + - - -
156F TRP* 2.9 26.1 + - - +
176F ALA* 3.5 13.2 - - + -
193F TRP* 3.3 30.9 - - - +
195F HIS* 5.1 0.2 - - - -
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Residues in contact with HIS 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F LEU* 3.8 17.5 - - + +
30F ARG 4.8 0.6 + - - -
33F ALA* 3.7 20.6 - - + +
34F GLU 3.3 26.4 + - - -
36F PRO* 4.4 0.4 - - + -
63F HIS* 3.0 31.8 + - - +
66F TYR* 4.3 9.0 - - + +
67F VAL* 3.5 14.8 - - + +
70F LEU* 4.2 5.4 - - + -
82F ILE* 3.5 33.2 - - + +
101F GLN 2.9 18.9 + - - +
102F ALA 3.6 4.5 - - - +
104F GLN* 1.3 75.9 - - - +
106F PHE* 1.3 60.7 + - - +
109F SER* 2.8 46.8 + - - -
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Residues in contact with PHE 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F THR* 3.6 22.7 - - + -
26F LEU* 3.8 24.9 - - + -
29F LEU* 3.8 15.0 - - + +
82F ILE* 4.1 5.2 - - + -
83F GLU* 3.7 36.6 - - + -
86F ILE* 3.6 19.5 - - + -
102F ALA 3.0 7.7 + - - +
103F ALA 3.5 6.3 - - - +
105F HIS* 1.3 76.9 - - - +
107F ASN* 1.3 68.8 + - - +
109F SER* 3.2 2.4 + - - -
110F PHE* 2.8 40.4 + + + +
158F TRP* 4.3 13.5 - + - -
178F CYS* 3.7 22.0 - - - -
180F LEU* 3.8 10.8 - - + -
186F PRO* 4.6 2.9 - - + -
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Residues in contact with ASN 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F ALA 2.8 25.6 + - - +
104F GLN* 3.3 16.5 + - - +
106F PHE* 1.3 85.3 - - - +
108F HIS* 1.3 59.6 + - - +
110F PHE* 3.4 3.1 + - - +
111F PHE* 2.9 27.9 + - - +
156F TRP* 3.4 34.6 - - + +
158F TRP* 3.2 30.0 - - + -
176F ALA 3.2 25.1 + - - -
177F GLY 3.7 4.4 + - - -
178F CYS* 3.5 7.3 - - - -
189F THR* 4.2 1.6 - - - +
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Residues in contact with HIS 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F HIS* 3.1 41.5 + + - -
62F HIS* 5.1 0.8 - - - +
63F HIS* 3.5 30.1 - + + +
66F TYR* 3.6 19.2 - + - -
104F GLN* 2.8 48.6 + - - +
107F ASN* 1.3 74.3 - - - +
109F SER* 1.3 64.4 + - - +
111F PHE* 3.1 7.8 + + - +
112F TRP* 2.9 37.7 + + - +
156F TRP* 3.5 19.9 - + - -
191F ASP* 3.3 10.1 + - - -
195F HIS* 3.7 6.2 + - - -
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Residues in contact with SER 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F LEU* 4.2 6.5 - - - -
28F HIS* 6.1 0.7 - - - -
29F LEU* 3.5 23.9 - - - +
36F PRO* 3.6 10.1 - - - +
63F HIS* 3.3 17.6 - - - -
105F HIS* 2.8 36.5 + - - -
106F PHE 3.6 3.4 - - - -
108F HIS* 1.3 75.2 - - - +
110F PHE* 1.3 62.8 + - - +
112F TRP* 3.4 7.6 + - - +
113F LYS* 3.4 25.6 + - - +
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Residues in contact with PHE 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F THR* 3.5 30.5 - - + -
26F LEU* 3.8 20.1 - - + +
106F PHE* 2.8 30.8 + + + +
107F ASN* 3.6 5.2 - - - +
109F SER* 1.3 74.9 - - - +
111F PHE* 1.3 60.9 + - - +
113F LYS* 3.2 14.5 + - - +
114F CYS* 3.2 25.2 + - - -
158F TRP* 4.1 7.9 - + - -
186F PRO* 3.6 19.1 - - + -
187F ILE* 3.6 22.7 - - - -
188F PHE* 3.6 22.9 - - - -
189F THR* 3.8 15.3 - - + -
220F PHE* 3.8 22.0 - + - -
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Residues in contact with PHE 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F MET* 4.1 10.3 - - + -
58F HIS* 4.0 15.9 - + - -
107F ASN 2.9 15.6 + - - +
108F HIS* 3.1 10.5 + + - +
110F PHE* 1.3 74.6 - - - +
112F TRP* 1.3 85.9 + + - +
114F CYS* 3.0 13.5 + - - +
115F LEU* 3.3 46.8 - - + +
156F TRP* 4.0 8.5 - + + -
189F THR* 3.4 35.4 - - + +
190F ALA* 3.8 3.4 - - - -
191F ASP* 3.6 30.5 - - + -
208F TYR* 3.5 21.3 - - - -
212F LEU* 4.5 6.3 - - + -
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Residues in contact with TRP 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36F PRO* 4.2 5.8 - - + -
38F LEU* 3.6 31.0 - - + -
39F GLY 5.8 0.2 + - - -
40F PHE* 4.2 9.6 - + + -
46F ILE* 4.6 4.0 - - + -
50F MET* 4.6 6.1 - - - -
55F LEU* 3.6 27.8 - - + -
58F HIS* 3.6 40.2 - + + -
59F TYR* 3.7 28.8 - + + -
63F HIS* 3.0 31.2 + + - -
108F HIS* 2.9 32.5 + + - +
109F SER* 3.4 7.4 + - - +
110F PHE 3.3 0.2 - - - -
111F PHE* 1.3 95.7 - + - +
113F LYS* 1.3 63.9 + - + +
115F LEU* 3.3 33.2 + - + +
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Residues in contact with LYS 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F LEU* 4.5 7.6 - - + -
28F HIS* 4.0 28.3 + - - +
36F PRO* 6.3 2.7 - - + -
37F THR 5.8 4.8 + - - +
109F SER 3.4 16.4 + - - +
110F PHE 3.2 6.1 + - - +
112F TRP* 1.3 79.0 - - + +
114F CYS* 1.3 59.7 + - - +
115F LEU 3.1 2.9 + - - +
217F ASP* 4.0 8.0 - - - +
220F PHE* 3.4 58.3 - - + +
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Residues in contact with CYS 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F PHE* 3.2 42.9 + - - -
111F PHE* 3.0 13.1 + - - +
113F LYS* 1.3 76.1 - - - +
115F LEU* 1.3 61.7 + - + +
187F ILE 4.3 0.9 - - - -
188F PHE* 3.8 34.5 - - + -
189F THR 3.8 7.6 - - - +
216F VAL* 3.4 11.3 - - - +
217F ASP* 2.8 26.3 + - - -
220F PHE* 4.0 14.8 - - - -
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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