Contacts of the helix formed by residues 15 - 24 (chain T) in PDB entry 4N3E
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 ALA 15 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17H HIS* 3.6 20.9 - - + +
159H ALA 5.3 1.6 - - - +
14T ILE* 1.3 79.0 - - - +
16T PRO* 1.4 63.0 - - + +
17T HIS* 3.1 30.5 - - + +
18T ARG* 2.8 33.7 + - - +
19T LEU* 3.3 8.0 + - - +
110T GLY 3.8 12.7 + - - +
111T GLY* 4.4 0.4 - - - -
112T SER* 4.2 0.2 + - - -
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Residues in contact with PRO 16 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H PRO* 6.4 0.9 - - + -
17H HIS* 5.8 1.1 - - - +
107H ALA* 4.7 1.3 - - + -
15T ALA* 1.4 87.0 - - + +
17T HIS* 1.3 62.6 - - + +
19T LEU* 3.9 1.6 - - + +
20T PHE* 2.9 33.8 + - - +
80T PHE* 3.4 41.2 - - + -
105T LEU* 3.8 16.5 - - + +
107T ALA* 3.8 23.6 - - + +
110T GLY 5.9 0.2 - - - -
111T GLY 4.0 10.8 - - - +
112T SER* 3.5 18.8 - - - +
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Residues in contact with HIS 17 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H ALA* 3.6 27.9 - - + +
16H PRO* 5.5 1.8 - - + +
17H HIS* 3.9 4.8 - + - -
18H ARG* 6.3 0.2 - - - -
109H GLY 3.6 24.5 + - - +
110H GLY* 3.6 22.4 + - - +
15T ALA* 3.1 30.7 - - + +
16T PRO* 1.3 88.0 - - + +
18T ARG* 1.3 66.2 + - + +
20T PHE* 4.4 2.4 - - - +
21T LYS* 3.3 24.1 + - - +
80T PHE* 4.2 5.2 - - + -
158T PHE 4.0 12.5 - - - +
159T ALA* 3.5 26.9 + - - -
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Residues in contact with ARG 18 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159H ALA 5.6 6.6 + - - -
14T ILE* 3.6 24.4 - - + +
15T ALA* 2.8 19.6 + - - +
17T HIS* 1.3 88.2 - - + +
19T LEU* 1.3 60.0 + - - +
20T PHE 3.2 0.2 - - - -
21T LYS* 3.4 1.7 + - - +
22T ALA* 3.0 32.4 + - - +
151T LEU* 3.0 54.5 + - + +
152T ALA* 4.9 0.6 - - - +
154T ASN 3.3 16.2 + - - -
155T PRO* 3.5 20.2 + - - +
157T VAL 2.9 26.3 + - - -
158T PHE* 3.4 30.4 - - + +
159T ALA* 4.5 3.3 - - - +
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Residues in contact with LEU 19 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12T SER* 3.9 25.6 - - - +
14T ILE* 4.2 23.1 - - + -
15T ALA 3.3 5.6 + - - +
16T PRO* 3.4 3.8 + - + +
18T ARG* 1.3 77.7 - - - +
20T PHE* 1.3 58.6 + - - +
22T ALA* 4.8 0.7 - - - -
23T LEU* 3.0 60.1 + - + +
24T VAL* 4.0 0.7 + - - +
105T LEU* 3.8 22.1 - - + +
112T SER* 4.1 15.5 - - - +
144T TYR* 4.5 17.5 - - + -
147T VAL* 5.4 0.7 - - + -
148T GLU* 5.3 4.7 - - - +
151T LEU* 4.5 10.3 - - + -
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Residues in contact with PHE 20 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16T PRO 2.9 18.5 + - - +
17T HIS* 4.4 4.0 - - - +
19T LEU* 1.3 79.7 - - - +
21T LYS* 1.3 57.7 + - - +
24T VAL* 3.4 30.5 + - + +
25T LEU* 3.0 54.8 + - + +
75T ILE* 5.1 2.2 - - + -
77T ALA* 4.2 22.7 - - + -
80T PHE* 3.5 35.7 - + + -
81T TYR 3.2 30.5 - - - -
82T CYS* 4.0 9.6 - - + -
103T VAL* 4.6 2.5 - - + -
105T LEU* 3.8 14.1 - - + +
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Residues in contact with LYS 21 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17T HIS 3.3 19.9 + - - +
18T ARG 3.4 3.3 + - - +
20T PHE* 1.3 78.6 - - - +
22T ALA* 1.3 57.1 + - - +
25T LEU* 3.1 43.1 - - + +
26T GLU* 2.7 55.3 + - + +
158T PHE* 4.2 31.2 - - + +
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Residues in contact with ALA 22 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18T ARG 3.0 17.7 + - - +
19T LEU* 4.4 2.0 - - - +
21T LYS* 1.3 76.6 - - - +
23T LEU* 1.3 60.8 + - + +
27T ARG* 3.5 8.5 - - - -
30T VAL* 3.0 37.0 - - + +
143T PHE* 4.4 1.0 - - - -
147T VAL* 3.8 26.0 - - + -
151T LEU* 4.3 4.3 - - + -
158T PHE* 3.5 21.8 - - + -
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Residues in contact with LEU 23 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19T LEU* 3.0 42.7 + - + +
22T ALA* 1.3 78.6 - - + +
24T VAL* 1.3 64.7 + - + +
27T ARG* 2.8 42.0 + - - +
84T TYR* 4.3 2.9 + - - -
143T PHE* 3.6 27.4 - - + -
144T TYR* 4.0 36.8 - - + -
147T VAL* 4.1 16.4 - - + -
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Residues in contact with VAL 24 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19T LEU 4.9 0.2 - - - +
20T PHE* 3.4 38.7 + - + +
23T LEU* 1.3 86.7 - - + +
25T LEU* 1.3 70.8 + - + +
26T GLU 3.5 1.5 + - - -
27T ARG* 3.6 13.9 + - - +
28T HIS* 4.9 0.2 - - - -
72T PHE* 3.6 16.9 - - + -
82T CYS* 3.5 36.6 - - + -
84T TYR* 4.4 13.2 - - + -
103T VAL* 4.0 26.9 - - + -
105T LEU* 5.8 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
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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