Contacts of the helix formed by residues 19 - 28 (chain I) in PDB entry 4XLN
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 THR 19 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I PRO* 3.3 6.6 - - - +
18I LEU* 1.3 76.5 + - - +
20I GLU* 1.3 64.7 + - - +
21I ILE 3.3 0.4 - - - -
22I GLN* 2.9 20.6 + - - +
23I VAL* 3.0 17.2 + - - +
123I GLU 4.5 5.5 + - - -
124I ASP* 3.5 34.8 - - + +
404I LEU* 4.1 12.1 - - + -
407I LYS* 4.5 10.3 - - + -
408I ARG* 6.0 0.2 - - - -
590I ASP* 3.4 27.0 + - - +
591I SER* 5.4 0.7 - - - -
592I LEU* 5.0 3.9 - - + +
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Residues in contact with GLU 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I PRO* 3.1 32.3 + - + +
18I LEU 3.2 0.9 - - - +
19I THR* 1.3 77.2 + - - +
21I ILE* 1.3 89.9 + - - +
22I GLN 2.8 5.2 + - - -
23I VAL* 3.0 2.4 + - - +
24I GLU* 2.6 56.8 + - + +
25I SER* 3.5 1.6 + - - -
460I ARG* 2.4 43.9 + - - +
461I VAL 4.9 5.5 + - - +
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Residues in contact with ILE 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I LEU 4.1 13.0 + - - +
20I GLU* 1.3 97.7 - - - +
22I GLN* 1.3 68.2 + - + +
25I SER* 3.7 20.5 - - - -
138I SER* 4.5 11.9 + - - +
333I ILE* 6.1 0.7 - - + -
335I THR* 4.0 20.9 - - + -
336I VAL* 3.8 7.6 + - - +
407I LYS* 4.2 19.5 - - + +
408I ARG* 4.8 5.8 - - + -
455I LEU* 4.7 19.1 - - + -
461I VAL* 3.7 42.4 - - + +
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Residues in contact with GLN 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I THR* 2.9 11.5 + - - +
20I GLU 2.8 1.2 + - - -
21I ILE* 1.3 84.1 + - + +
23I VAL* 1.3 63.9 + - - +
26I TYR* 3.1 21.0 + - - +
121I MET* 3.3 27.6 - - + +
124I ASP 5.0 0.2 - - - +
125I GLY* 3.7 17.0 - - - +
135I VAL* 4.1 5.7 - - - +
136I ILE* 3.2 29.0 + - - +
138I SER* 4.3 10.5 + - - +
336I VAL* 3.2 24.2 - - - +
407I LYS* 3.4 45.4 + - + +
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Residues in contact with VAL 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I THR* 3.0 14.9 + - - +
20I GLU* 3.0 4.1 + - - -
22I GLN* 1.3 73.2 - - - +
24I GLU* 1.3 68.3 + - + +
26I TYR* 2.9 7.3 + - + +
27I LYS* 2.8 28.4 + - + +
121I MET* 3.7 10.5 - - + -
122I THR 4.1 8.7 - - - +
123I GLU* 3.7 24.2 - - - +
124I ASP 4.4 0.7 - - - -
125I GLY* 3.7 22.0 - - - +
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Residues in contact with GLU 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I GLU* 2.6 42.7 + - + +
23I VAL* 1.3 80.2 - - + +
25I SER* 1.3 56.3 + - - +
27I LYS* 2.9 54.7 + - - +
28I LYS* 3.3 8.3 + - - +
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Residues in contact with SER 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I GLU* 3.5 4.0 + - - -
21I ILE* 3.7 26.9 - - - -
23I VAL 3.4 0.2 - - - -
24I GLU* 1.3 77.2 - - - +
26I TYR* 1.3 58.2 + - - +
28I LYS* 3.2 35.7 - - - +
335I THR* 2.9 35.7 + - - +
336I VAL* 4.5 0.9 - - - -
337I GLY* 3.5 14.4 - - - -
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Residues in contact with TYR 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I GLN 3.1 21.9 + - - +
23I VAL* 2.9 7.4 + - + +
25I SER* 1.3 75.9 - - - +
27I LYS* 1.3 64.2 + - - +
29I ALA* 3.4 3.3 + - + -
30I LEU* 3.2 63.1 + - + +
118I LEU* 4.3 3.1 - - - +
119I PRO 2.6 26.3 + - - -
120I LEU* 3.9 2.1 - - - -
121I MET* 3.5 43.7 - - + -
127I PHE* 3.3 20.1 - + - -
336I VAL* 4.0 6.9 - - + +
337I GLY* 4.1 14.4 - - - -
340I MET* 3.6 34.2 - - + +
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Residues in contact with LYS 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I VAL* 2.8 14.4 + - + +
24I GLU* 2.9 39.0 + - - +
26I TYR* 1.3 73.8 - - - +
28I LYS* 1.3 60.3 + - - +
29I ALA 3.1 2.0 - - - -
30I LEU* 2.8 27.7 + - + -
31I GLN* 3.0 16.8 + - - +
34I VAL* 6.0 6.5 - - - -
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Residues in contact with LYS 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24I GLU 3.3 4.9 + - - +
25I SER* 3.2 40.9 + - - +
27I LYS* 1.3 81.0 - - - +
29I ALA* 1.3 60.4 + - - +
30I LEU 3.2 0.7 + - - -
31I GLN* 3.6 18.2 + - - +
40I GLU* 5.5 2.1 - - - +
42I VAL* 3.8 15.7 - - - +
43I GLY* 5.3 5.4 - - - +
335I THR* 4.3 4.3 - - - -
337I GLY 4.4 2.2 - - - -
338I GLU* 3.5 38.5 + - - +
463I ALA* 4.6 28.5 + - + +
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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