Contacts of the helix formed by residues 95 - 114 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E THR* 3.9 27.0 - - - +
92E ILE* 2.8 25.4 + - - +
94E GLU* 1.3 81.2 + - - +
96E LYS* 1.3 57.3 + - - +
97E VAL 3.2 3.3 + - - +
98E MET* 3.3 17.4 + - - +
99E PHE* 2.8 30.5 + - - +
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Residues in contact with LYS 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92E ILE 3.2 6.9 + - - +
93E ASN* 3.3 16.2 + - - +
94E GLU 3.5 1.0 - - - -
95E SER* 1.3 77.7 - - - +
97E VAL* 1.3 64.8 + - + +
99E PHE* 3.5 6.4 + - - +
100E ASN* 3.0 34.0 + - - +
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Residues in contact with VAL 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E LYS* 4.2 15.5 - - - -
73E LEU* 3.8 21.1 - - + -
94E GLU 5.2 0.8 + - - -
95E SER* 3.2 0.8 - - - +
96E LYS* 1.3 80.3 - - + +
98E MET* 1.3 62.8 + - - +
100E ASN* 3.2 9.3 + - - +
101E GLN* 3.1 39.2 + - - +
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Residues in contact with MET 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E LEU* 4.0 10.3 - - + -
73E LEU* 3.6 46.1 - - + +
74E GLY* 4.0 13.9 - - - -
77E TYR* 4.2 14.1 - - + +
85E ILE* 4.0 26.0 - - + -
89E THR* 4.1 16.4 - - + -
95E SER* 3.3 19.4 + - - +
97E VAL* 1.3 75.1 - - - +
99E PHE* 1.3 66.8 + - - +
101E GLN* 3.3 3.0 + - - +
102E ALA* 2.9 23.1 + - - +
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Residues in contact with PHE 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E ILE* 3.6 27.6 - - + -
89E THR* 3.4 31.3 + - - +
90E THR* 3.7 31.4 - - - -
91E GLY 5.6 0.9 - - - -
95E SER 2.8 18.3 + - - +
96E LYS* 3.8 6.5 - - - +
98E MET* 1.3 76.3 - - - +
100E ASN* 1.3 73.3 + - - +
102E ALA* 4.7 1.8 - - - -
103E ALA* 2.8 52.8 + - + +
176E ALA* 4.4 13.9 - - + -
177E GLY* 4.8 3.4 - - - -
178E CYS* 4.8 5.6 - - + -
181E THR* 4.0 8.7 - - + -
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Residues in contact with ASN 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E LYS* 3.0 22.0 + - - +
97E VAL* 3.2 11.8 + - - +
99E PHE* 1.3 85.7 - - - +
101E GLN* 1.3 62.2 + - - +
104E GLN* 2.9 36.8 + - - +
175E ASN* 5.8 0.2 - - - +
176E ALA* 3.6 17.0 + - - +
152F PHE* 3.3 50.6 - - + +
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Residues in contact with GLN 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E ALA 4.2 0.5 - - - +
66E TYR* 3.4 45.6 - - - +
69E LYS* 3.2 38.4 - - + +
70E LEU* 3.9 14.6 - - + +
73E LEU* 4.3 6.1 - - + -
97E VAL* 3.1 28.3 + - + +
98E MET 3.8 3.6 - - - +
100E ASN* 1.3 85.3 - - - +
102E ALA* 1.3 58.7 + - - +
104E GLN* 3.8 0.9 - - - +
105E HIS* 2.9 30.5 + - - +
152F PHE* 4.6 8.3 - - - -
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Residues in contact with ALA 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E LEU* 3.8 20.8 - - + +
82E ILE* 3.3 13.3 - - + +
85E ILE* 3.7 28.5 - - + -
86E ILE* 3.9 15.5 - - + +
98E MET 2.9 20.7 + - - +
99E PHE* 3.9 2.5 - - - +
101E GLN* 1.3 73.9 - - - +
103E ALA* 1.3 58.0 + - - +
105E HIS* 3.3 1.3 + - - +
106E PHE* 3.0 24.9 + - - +
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Residues in contact with ALA 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E ILE* 3.7 13.6 - - + +
99E PHE* 2.8 39.9 + - + +
102E ALA* 1.3 72.9 - - - +
104E GLN* 1.3 57.8 + - - +
106E PHE* 3.3 2.9 + - - +
107E ASN* 2.8 36.1 + - - +
176E ALA* 3.2 28.9 - - + +
178E CYS* 4.4 6.5 - - + -
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Residues in contact with GLN 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E TYR* 3.0 52.4 + - + -
100E ASN 2.9 22.1 + - - +
103E ALA* 1.3 73.4 - - - +
105E HIS* 1.3 64.3 + - - +
107E ASN* 3.3 7.6 + - - +
108E HIS* 2.8 45.7 + - - -
156E TRP* 2.9 25.3 + - - +
176E ALA* 3.5 19.1 - - + -
193E TRP* 3.4 25.3 - - - +
152F PHE* 3.9 4.0 - - + -
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Residues in contact with HIS 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E LEU* 3.7 16.2 - - + +
30E ARG 5.0 0.8 + - - -
33E ALA* 3.7 26.6 - - + +
34E GLU 3.3 26.8 + - - -
36E PRO* 4.3 0.4 - - + -
63E HIS* 2.7 35.0 + + + +
66E TYR* 4.4 6.4 - - + +
67E VAL* 3.6 13.4 - - + +
70E LEU* 4.4 4.5 - - + -
82E ILE* 3.7 23.9 - - + +
101E GLN 2.9 22.4 + - - +
102E ALA* 3.3 5.8 + - - +
104E GLN* 1.3 71.7 - - - +
106E PHE* 1.3 62.0 + - - +
109E SER* 2.9 47.3 + - - -
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Residues in contact with PHE 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E THR* 3.6 28.0 - - + -
26E LEU* 3.8 20.4 - - + -
29E LEU* 3.9 13.9 - - + -
82E ILE* 4.1 6.2 - - + +
83E GLU* 3.5 38.6 - - + -
86E ILE* 3.6 19.5 - - + -
102E ALA 3.0 7.6 + - - +
103E ALA 3.6 5.8 - - - +
105E HIS* 1.3 76.7 - - - +
107E ASN* 1.3 81.1 + - - +
109E SER* 3.2 1.7 + - - -
110E PHE* 2.9 34.2 + - + +
158E TRP* 4.4 9.0 - + - -
178E CYS* 3.7 10.5 - - - -
180E LEU* 3.9 15.0 - - + -
186E PRO* 4.3 8.7 - - + -
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Residues in contact with ASN 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E ALA 2.8 23.5 + - - +
104E GLN* 3.3 14.9 + - - +
106E PHE* 1.3 85.6 - - - +
108E HIS* 1.3 59.1 + - - +
110E PHE* 3.7 2.5 - - - +
111E PHE* 2.9 28.1 + - - +
156E TRP* 3.4 36.2 - - + +
158E TRP* 3.3 26.0 - - + -
176E ALA 3.1 26.1 + - - -
177E GLY 3.6 6.3 + - - -
178E CYS* 3.5 8.7 - - - -
189E THR* 4.2 1.9 - - - +
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Residues in contact with HIS 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E HIS* 3.1 40.6 + + - -
62E HIS* 5.0 1.0 - - - +
63E HIS* 3.5 30.1 - + + +
66E TYR* 3.6 18.2 - + - -
104E GLN* 2.8 47.6 + - - +
107E ASN* 1.3 77.1 - - - +
109E SER* 1.3 65.9 + - - +
111E PHE* 3.2 5.5 + + - +
112E TRP* 2.9 38.4 + + - +
156E TRP* 3.5 23.8 - + - -
191E ASP* 3.4 8.7 + - - -
195E HIS* 3.8 5.6 + - - -
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Residues in contact with SER 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E LEU* 4.2 6.1 - - - -
29E LEU* 3.6 23.3 - - - +
36E PRO* 3.7 11.3 - - - +
63E HIS* 3.3 10.5 - - - -
105E HIS* 2.9 44.4 + - - -
106E PHE 3.7 3.4 - - - -
108E HIS* 1.3 77.6 - - - +
110E PHE* 1.3 62.7 + - - +
112E TRP* 3.4 8.6 + - - +
113E LYS* 3.4 24.4 + - - +
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Residues in contact with PHE 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E THR* 3.5 31.6 - - + -
26E LEU* 3.8 13.8 - - + +
106E PHE* 2.9 27.6 + + + +
107E ASN* 3.7 3.6 - - - +
109E SER* 1.3 74.4 - - - +
111E PHE* 1.3 64.9 + - - +
113E LYS* 3.0 16.3 + - - +
114E CYS* 3.2 23.7 + - - -
158E TRP* 4.0 8.1 - + - -
186E PRO* 3.5 20.4 - - + -
187E ILE* 3.4 25.4 - - - -
188E PHE* 3.6 22.4 - - - -
189E THR* 3.8 15.5 - - + -
220E PHE* 3.6 29.2 - + - -
224E MET* 4.0 2.9 - - + -
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Residues in contact with PHE 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E MET* 3.9 11.2 - - + -
58E HIS* 3.9 16.4 - + - -
107E ASN 2.9 17.8 + - - +
108E HIS* 3.4 7.0 - + - +
110E PHE* 1.3 74.3 - - - +
112E TRP* 1.3 82.5 + + - +
114E CYS* 2.9 25.4 + - + +
115E LEU* 3.4 40.9 - - + +
156E TRP* 3.9 11.0 - + + -
189E THR* 3.4 32.4 - - + +
190E ALA* 3.9 3.8 - - - -
191E ASP* 3.6 30.7 - - + -
196E ALA* 5.2 0.2 - - + -
208E TYR* 3.6 22.0 - - - -
212E LEU* 4.6 4.9 - - + -
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Residues in contact with TRP 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E PRO* 3.9 15.3 - - + -
38E LEU* 3.4 32.8 - - + -
39E GLY 5.5 1.2 + - - -
40E PHE* 4.2 9.1 - + + -
46E ILE* 4.6 5.4 - - + -
50E MET* 4.8 3.6 - - - -
55E LEU* 3.6 28.7 - - + -
58E HIS* 3.5 38.8 - + + -
59E TYR* 3.6 27.8 - + + -
63E HIS* 2.9 27.4 + - - -
108E HIS* 2.9 36.8 + + - -
109E SER* 3.8 4.0 - - - +
110E PHE 3.3 0.4 - - - -
111E PHE* 1.3 91.8 - + - +
113E LYS* 1.3 63.4 + - + +
115E LEU* 3.3 33.2 + - + +
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Residues in contact with LYS 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E LEU* 4.1 19.5 - - + -
36E PRO* 6.2 2.2 - - - +
37E THR 4.9 10.5 + - - -
109E SER 3.4 13.7 + - - +
110E PHE* 3.0 7.4 + - - +
112E TRP* 1.3 77.6 - - + +
114E CYS* 1.3 59.9 + - - +
115E LEU 3.2 2.6 + - - +
217E ASP* 3.8 8.5 - - - +
220E PHE* 3.5 57.2 - - + +
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Residues in contact with CYS 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E PHE* 3.2 42.8 + - - -
111E PHE* 2.9 15.1 + - - +
113E LYS* 1.3 77.4 - - - +
115E LEU* 1.3 56.3 + - + +
187E ILE 4.2 0.9 - - - -
188E PHE* 3.8 35.0 - - + -
189E THR 3.8 7.2 - - - +
216E VAL* 3.3 11.4 - - - +
217E ASP* 2.7 29.6 + - - -
220E PHE* 4.0 15.3 - - - -
221E VAL* 4.7 0.9 - - - -
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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