Contacts of the helix formed by residues 95 - 114 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B ALA 5.3 0.2 + - - -
89B THR* 3.8 31.2 - - - +
92B ILE* 3.0 27.0 + - - +
94B GLU* 1.3 80.2 + - - +
96B LYS* 1.3 58.9 + - - +
97B VAL 3.3 3.0 + - - -
98B MET* 3.3 11.7 + - - +
99B PHE* 2.9 28.5 + - - +
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Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A PHE* 6.2 0.4 - - - -
91B GLY 6.3 1.3 - - - +
92B ILE 3.5 5.6 + - - +
93B ASN* 3.4 20.0 + - - +
94B GLU 3.5 1.2 - - - -
95B SER* 1.3 77.0 - - - +
97B VAL* 1.3 64.4 + - + +
99B PHE* 3.6 21.4 - - + +
100B ASN* 2.9 61.0 + - - +
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LYS* 4.4 16.4 - - - -
73B LEU* 4.0 21.8 - - + -
94B GLU 5.3 1.0 + - - +
95B SER 3.3 0.8 - - - -
96B LYS* 1.3 80.2 - - + +
98B MET* 1.3 63.9 + - - +
100B ASN* 3.3 7.2 + - - +
101B GLN* 3.2 26.1 + - + +
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Residues in contact with MET 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LEU* 4.1 9.9 - - + -
73B LEU* 3.5 50.2 - - + +
74B GLY* 3.9 9.9 - - - -
77B TYR* 4.2 15.7 - - + +
85B ILE* 3.9 23.1 - - + -
89B THR* 3.8 20.4 - - + -
95B SER* 3.3 14.3 + - - +
97B VAL* 1.3 76.3 - - - +
99B PHE* 1.3 68.4 + - - +
101B GLN* 3.2 2.1 + - - +
102B ALA* 2.9 22.0 + - - +
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Residues in contact with PHE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ILE* 3.8 21.5 - - + -
89B THR* 3.4 30.0 + - - +
90B THR* 3.7 37.7 - - - -
91B GLY 5.6 0.7 - - - -
95B SER 2.9 16.9 + - - +
96B LYS* 3.6 22.0 - - + +
97B VAL 3.3 0.2 - - - -
98B MET* 1.3 76.4 - - - +
100B ASN* 1.3 75.9 + - - +
102B ALA* 3.8 1.9 - - - +
103B ALA* 2.8 49.0 + - + +
176B ALA* 4.2 14.4 - - + -
177B GLY* 4.8 7.4 - - - -
178B CYS* 5.1 1.3 - - + -
181B THR* 4.1 7.4 - - + -
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Residues in contact with ASN 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PHE* 3.7 48.0 - - + +
96B LYS* 2.9 54.1 + - - +
97B VAL* 3.7 7.1 - - - +
99B PHE* 1.3 82.2 - - - +
101B GLN* 1.3 61.7 + - - +
104B GLN* 3.0 35.8 + - - +
175B ASN* 5.7 0.3 - - - +
176B ALA* 3.6 14.0 + - - +
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Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A PHE* 4.4 8.1 - - - -
65B ALA 4.0 1.0 - - - +
66B TYR* 3.3 39.3 - - - +
69B LYS* 3.2 40.6 - - + +
70B LEU* 4.0 22.8 - - + +
73B LEU* 4.2 6.5 - - + -
97B VAL* 3.2 19.0 + - + +
98B MET 3.2 5.6 + - - +
100B ASN* 1.3 84.5 - - - +
102B ALA* 1.3 58.3 + - - +
104B GLN* 3.9 1.0 - - - +
105B HIS* 2.9 30.7 + - - +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B LEU* 3.9 19.6 - - + +
82B ILE* 3.4 13.8 - - + +
85B ILE* 3.7 29.2 - - + -
86B ILE* 3.9 15.5 - - + +
98B MET 2.9 16.8 + - - +
99B PHE* 3.8 3.4 - - - +
101B GLN* 1.3 75.3 - - - +
103B ALA* 1.3 58.8 + - - +
105B HIS* 3.2 1.7 + - - +
106B PHE* 2.9 25.5 + - - +
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ILE* 3.7 19.2 - - + +
99B PHE* 2.8 35.3 + - + +
102B ALA* 1.3 74.0 - - - +
104B GLN* 1.3 51.3 + - - +
106B PHE* 3.2 1.6 + - - +
107B ASN* 2.7 41.9 + - - +
176B ALA* 3.2 29.4 - - + +
178B CYS* 4.6 5.2 - - + -
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Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A PHE* 3.8 10.3 - - + -
66B TYR* 3.1 53.8 + - + -
100B ASN 3.0 23.1 + - - +
103B ALA* 1.3 75.7 - - - +
105B HIS* 1.3 62.2 + - - +
107B ASN* 3.2 12.5 + - - +
108B HIS* 2.8 46.6 + - - -
156B TRP* 2.9 26.3 + - - -
175B ASN 3.6 2.4 - - - +
176B ALA* 3.6 5.4 - - + -
193B TRP* 3.3 30.9 - - - +
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Residues in contact with HIS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 3.7 15.5 - - + +
30B ARG 4.9 0.6 + - - -
33B ALA* 3.7 22.4 - - + +
34B GLU 3.3 28.7 + - - -
36B PRO* 4.4 0.9 - - + -
63B HIS* 3.0 29.4 + - - +
66B TYR* 4.4 8.4 - - + +
67B VAL* 3.5 16.0 - - + +
70B LEU* 4.1 6.7 - - + -
82B ILE* 3.7 28.3 - - + +
101B GLN 2.9 19.7 + - - +
102B ALA 3.6 4.0 - - - +
104B GLN* 1.3 76.0 - - - +
106B PHE* 1.3 63.2 + - - +
109B SER* 2.9 44.8 + - - -
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Residues in contact with PHE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B THR* 3.7 21.8 - - + -
26B LEU* 3.8 22.9 - - + -
29B LEU* 3.7 15.2 - - + +
82B ILE* 4.1 5.6 - - + -
83B GLU* 3.5 36.8 - - + -
86B ILE* 3.6 13.5 - - + -
102B ALA 2.9 15.2 + - - +
103B ALA 3.6 2.7 - - - +
105B HIS* 1.3 77.7 - - - +
107B ASN* 1.3 77.9 + - - +
109B SER* 3.2 2.4 + - - -
110B PHE* 2.9 32.1 + + + +
158B TRP* 4.4 13.0 - + - -
178B CYS* 3.8 14.4 - - - -
180B LEU* 3.5 21.3 - - + -
186B PRO* 4.9 2.9 - - + -
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Residues in contact with ASN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ALA 2.7 24.6 + - - +
104B GLN* 3.2 21.2 + - - +
106B PHE* 1.3 83.6 - - - +
108B HIS* 1.3 58.6 + - - +
110B PHE* 3.4 3.4 + - - +
111B PHE* 3.0 27.2 + - - +
156B TRP* 3.3 39.0 - - + +
158B TRP* 3.2 29.5 - - + -
176B ALA 3.2 21.0 + - - -
177B GLY 3.8 2.2 + - - -
178B CYS* 3.6 7.4 - - - -
189B THR* 4.2 2.1 - - - +
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Residues in contact with HIS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B HIS* 3.1 42.4 + + - -
62B HIS* 5.0 0.8 - - - +
63B HIS* 3.4 30.7 - + + +
66B TYR* 3.6 28.7 - + - -
104B GLN* 2.8 35.6 + - - +
107B ASN* 1.3 75.6 - - - +
109B SER* 1.3 65.0 + - - +
111B PHE* 3.2 6.0 + + - +
112B TRP* 3.0 38.1 + + - +
156B TRP* 3.5 22.8 - + - -
191B ASP* 3.4 8.9 + - - -
195B HIS* 3.6 6.6 + + - -
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Residues in contact with SER 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 4.0 6.5 - - - -
28B HIS* 6.1 0.2 - - - -
29B LEU* 3.5 24.7 - - - +
36B PRO* 3.7 10.8 - - - +
63B HIS* 3.5 5.9 - - - -
105B HIS* 2.9 39.9 + - - -
106B PHE 3.6 4.0 - - - -
108B HIS* 1.3 75.6 - - - +
110B PHE* 1.3 62.9 + - - +
112B TRP* 3.4 11.4 + - - +
113B LYS* 3.3 25.8 + - - +
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Residues in contact with PHE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B THR* 3.6 29.6 - - + -
26B LEU* 3.8 21.0 - - + +
106B PHE* 2.9 27.6 + + + +
107B ASN* 3.7 4.7 - - - +
109B SER* 1.3 75.6 - - - +
111B PHE* 1.3 63.7 + - - +
113B LYS* 3.1 14.9 + - - +
114B CYS* 3.1 20.2 + - - -
158B TRP* 4.0 8.1 - + - -
186B PRO* 3.7 19.3 - - + -
187B ILE* 3.5 24.5 - - - -
188B PHE* 3.6 27.4 - - - -
189B THR* 3.8 16.4 - - + -
220B PHE* 3.7 22.7 - + - -
224B MET* 4.2 3.4 - - + -
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Residues in contact with PHE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B MET* 4.0 12.8 - - + -
58B HIS* 4.1 15.7 - + - -
107B ASN 3.0 14.1 + - - +
108B HIS* 3.3 10.3 - + - +
110B PHE* 1.3 76.1 - - - +
112B TRP* 1.3 81.9 + + - +
114B CYS* 3.1 14.1 + - + +
115B LEU* 3.3 46.7 - - + +
156B TRP* 4.0 11.0 - + + -
189B THR* 3.3 34.9 - - + +
190B ALA* 3.7 3.4 - - - -
191B ASP* 3.6 27.8 - - + -
196B ALA* 5.1 0.2 - - + -
208B TYR* 3.5 22.2 - - - -
212B LEU* 4.5 6.3 - - + -
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Residues in contact with TRP 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PRO* 3.9 13.5 - - + -
38B LEU* 3.6 31.6 - - + -
39B GLY 5.7 0.9 + - - -
40B PHE* 4.3 7.2 - + + -
46B ILE* 4.6 5.8 - - + -
50B MET* 4.8 3.1 - - - -
55B LEU* 3.7 26.7 - - + -
58B HIS* 3.6 38.4 - + + -
59B TYR* 3.7 27.3 - + + -
63B HIS* 2.9 30.3 + + - -
108B HIS* 3.0 28.6 + + + -
109B SER* 3.9 4.0 - - - +
110B PHE 3.3 0.2 - - - -
111B PHE* 1.3 95.0 - + - +
113B LYS* 1.3 63.0 + - + +
115B LEU* 3.2 36.0 + - + +
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU* 4.7 7.2 - - + -
28B HIS* 4.6 21.9 + - - +
36B PRO* 6.5 0.9 - - + -
37B THR 5.8 3.4 - - - +
109B SER 3.3 15.4 + - - +
110B PHE* 3.1 10.2 + - - +
112B TRP* 1.3 77.8 - - + +
114B CYS* 1.3 59.2 + - - +
115B LEU 3.2 2.7 + - - +
217B ASP* 3.8 7.8 - - - +
220B PHE* 3.3 58.2 - - + +
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Residues in contact with CYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B PHE* 3.1 41.7 + - - -
111B PHE* 3.1 14.1 + - - +
113B LYS* 1.3 75.8 - - - +
115B LEU* 1.3 57.3 + - + +
187B ILE 4.3 0.7 - - - -
188B PHE* 3.7 35.7 - - + -
189B THR 3.9 6.7 - - - +
216B VAL* 3.3 11.1 - - - +
217B ASP* 2.7 29.8 + - - -
220B PHE* 4.0 15.5 - - - -
221B VAL* 4.8 1.1 - - - -
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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