Contacts of the helix formed by residues 31 - 48 (chain G) 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 GLY 31 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G GLU 3.2 1.4 + - - -
30G ARG* 1.3 74.4 - - - +
32G PHE* 1.3 59.0 + - - +
33G GLY 3.1 6.5 + - - -
34G VAL* 3.4 15.1 + - - +
35G THR* 3.6 3.2 + - - -
193G ASP* 3.4 19.5 + - - -
42H ARG* 3.2 28.6 + - - -
938I LYS* 4.4 4.5 - - - +
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Residues in contact with PHE 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G LEU* 4.3 6.5 - - + -
29G GLU* 2.9 45.7 + - + +
30G ARG 3.0 3.9 + - - -
31G GLY* 1.3 76.2 - - - +
33G GLY* 1.3 63.5 - - - +
34G VAL 3.3 0.2 - - - -
35G THR* 3.3 25.6 + - + -
36G LEU* 3.3 32.2 - - + +
42H ARG 4.7 0.2 - - - -
43H ILE* 3.5 31.2 - - + -
46H SER* 3.3 27.8 - - - -
47H SER* 3.7 15.5 - - - -
217H ILE* 4.4 6.1 - - + -
221H HIS* 3.7 34.3 - + - -
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Residues in contact with GLY 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G LEU* 4.0 18.6 - - - +
31G GLY 3.1 2.2 - - - -
32G PHE* 1.3 79.3 - - - +
34G VAL* 1.3 58.0 + - - +
36G LEU 3.5 0.3 + - - -
37G GLY* 2.9 26.0 + - - -
179G PHE* 4.0 0.5 - - - -
181G VAL* 3.6 23.1 - - - -
193G ASP* 4.2 10.7 - - - +
195G LEU* 3.2 11.9 - - - +
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Residues in contact with VAL 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G GLY* 3.8 14.8 - - - +
32G PHE 3.3 0.4 - - - -
33G GLY* 1.3 75.0 - - - +
35G THR* 1.3 64.0 + - - +
36G LEU 3.0 0.2 + - - -
38G ASN* 3.0 23.6 + - + -
39G PRO* 3.4 4.3 - - - +
179G PHE* 3.6 15.0 - - + -
181G VAL* 3.9 12.8 - - + +
42H ARG* 4.5 14.1 - - - +
939I ARG* 4.0 24.7 - - + -
979I THR 4.6 2.6 - - - +
980I GLY* 3.3 36.8 - - - +
981I GLU* 3.9 7.9 - - + +
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Residues in contact with THR 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G GLY 3.6 7.3 + - - -
32G PHE* 3.3 20.1 + - + -
34G VAL* 1.3 78.4 - - - +
36G LEU* 1.3 64.5 + - + +
39G PRO* 3.1 22.1 - - - +
38H ASN* 6.3 0.2 - - - -
39H PRO* 3.6 39.6 - - + +
42H ARG* 2.8 39.1 + - + +
43H ILE* 4.0 15.3 - - + -
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Residues in contact with LEU 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G LEU* 4.5 11.7 - - + -
28G LEU* 3.6 38.4 - - + -
32G PHE* 3.3 34.7 + - + +
33G GLY 4.4 0.7 - - - +
34G VAL 3.1 0.4 - - - -
35G THR* 1.3 85.6 - - + +
37G GLY* 1.3 67.7 + - - +
38G ASN 3.4 0.2 - - - -
39G PRO* 3.1 13.4 - - - +
40G LEU* 3.4 20.1 + - + +
195G LEU* 4.0 8.3 - - + -
218G LEU* 5.7 1.0 - - - +
43H ILE* 5.5 4.3 - - + -
218H LEU* 5.9 4.9 - - + +
221H HIS* 4.1 24.7 - - + +
222H LEU* 5.4 14.9 - - + +
225H PHE* 5.8 6.5 - - + -
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Residues in contact with GLY 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G GLY 2.9 20.7 + - - -
36G LEU* 1.3 74.9 - - - +
38G ASN* 1.3 60.4 + - - +
40G LEU* 3.6 4.6 + - - +
41G ARG* 3.2 19.9 + - - +
179G PHE* 3.8 17.4 - - - -
195G LEU* 3.5 16.7 - - - +
197G LEU* 4.2 11.6 - - - +
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Residues in contact with ASN 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G VAL 3.0 14.9 + - - +
37G GLY* 1.3 69.3 - - - -
39G PRO* 1.3 69.2 - - + +
41G ARG* 3.0 31.4 + - - +
42G ARG* 3.1 19.9 + - - +
179G PHE* 3.5 30.0 - - + -
860I HIS* 4.3 6.9 - - - -
976I ASP 4.3 2.0 + - - -
977I GLY 3.5 16.9 + - - +
979I THR 2.8 29.7 - - - +
980I GLY* 3.3 16.9 - - - +
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Residues in contact with PRO 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G VAL 3.4 5.2 - - - +
35G THR* 3.1 24.9 - - - +
36G LEU* 3.1 10.1 - - - +
38G ASN* 1.3 93.1 - - + +
40G LEU* 1.3 60.5 - - - +
42G ARG* 3.2 13.4 + - + -
43G ILE* 3.2 22.0 + - + +
218G LEU* 5.2 11.2 - - + -
35H THR* 3.3 29.2 - - + +
38H ASN* 5.8 1.1 - - + -
39H PRO* 3.4 23.3 - - + -
979I THR 4.8 3.1 - - - +
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Residues in contact with LEU 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G LEU* 3.4 12.6 + - + +
37G GLY* 3.8 8.3 - - - +
38G ASN 3.2 0.8 - - - -
39G PRO* 1.3 80.1 - - - +
41G ARG* 1.3 53.1 + - - +
43G ILE* 3.4 5.3 + - + +
44G LEU* 2.8 38.7 + - - +
197G LEU* 4.4 12.1 - - + -
211G LEU* 3.8 22.4 - - + -
214G ALA* 3.9 13.5 - - + +
215G VAL* 3.7 37.9 - - + +
218G LEU* 3.7 28.3 - - + -
222H LEU* 5.3 4.3 - - + -
225H PHE* 4.2 20.6 - - + -
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Residues in contact with ARG 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G GLY 3.2 11.3 + - - +
38G ASN* 3.0 26.1 + - - +
40G LEU* 1.3 79.8 - - - +
42G ARG* 1.3 57.3 + - - +
44G LEU* 3.3 6.7 + - - +
45G LEU* 2.9 51.7 + - + +
177G VAL* 3.4 38.0 + - + +
179G PHE* 4.8 8.1 - - + -
197G LEU* 5.3 1.1 - - - +
855I VAL 5.2 1.6 + - - -
856I GLU 3.4 20.8 + - - -
858I MET* 4.2 1.8 + - - +
860I HIS* 3.2 54.9 + - - +
864I GLY 3.7 13.3 + - - -
866I PRO* 4.9 7.9 - - - +
977I GLY* 3.7 13.1 + - - -
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Residues in contact with ARG 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G ASN* 3.1 26.2 + - - +
39G PRO* 3.2 7.4 + - - +
41G ARG* 1.3 79.0 - - + +
43G ILE* 1.3 59.2 + - - +
45G LEU* 3.3 5.3 + - - +
46G SER* 2.8 29.0 + - - -
31H GLY* 2.7 27.1 + - - -
32H PHE* 5.2 0.9 - - - -
34H VAL* 4.3 6.8 - - - +
35H THR* 2.5 41.4 + - - +
856I GLU* 4.0 18.4 + - + +
857I ASP* 3.2 45.7 + - - +
977I GLY 2.5 37.6 + - - +
978I ARG* 3.4 14.0 - - - +
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Residues in contact with ILE 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G PRO 3.2 17.0 + - - +
40G LEU* 3.9 4.7 - - - +
42G ARG* 1.3 76.4 - - - +
44G LEU* 1.3 57.7 + - - +
46G SER* 3.3 5.8 - - - -
47G SER* 3.0 26.4 + - - -
48G ILE* 4.0 4.5 + - - +
214G ALA* 4.0 12.3 - - + +
217G ILE* 3.8 37.9 - - + -
218G LEU* 3.6 47.3 - - + -
32H PHE* 3.6 24.0 - - + -
35H THR* 3.8 11.7 - - + -
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Residues in contact with LEU 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40G LEU 2.8 19.6 + - - +
41G ARG* 3.5 5.6 - - - +
43G ILE* 1.3 77.0 - - - +
45G LEU* 1.3 57.8 + - - +
46G SER 3.1 3.3 + - - -
48G ILE* 3.1 20.2 - - + +
172G SER* 4.8 0.2 + - - -
174G VAL* 3.1 43.7 - - + +
177G VAL* 3.7 21.1 - - + -
197G LEU* 4.3 10.5 - - + -
199G ILE* 3.6 29.8 - - + -
210G ALA* 4.1 20.9 - - + +
211G LEU* 4.5 12.1 - - + -
214G ALA* 4.3 13.6 - - + +
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Residues in contact with LEU 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G ARG* 2.9 60.8 + - + +
42G ARG 3.3 3.3 + - - +
44G LEU* 1.3 75.8 - - - +
46G SER* 1.3 56.9 + - - +
172G SER* 3.6 15.4 + - - -
174G VAL* 3.7 25.1 - - + +
175G ARG 4.6 4.3 - - - +
176G ARG* 4.1 6.3 - - - -
177G VAL* 3.7 29.6 - - + +
855I VAL* 4.3 25.5 - - + +
856I GLU* 4.4 17.7 - - - +
864I GLY 5.5 1.1 - - - +
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Residues in contact with SER 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G ARG 2.8 20.4 + - - -
43G ILE* 3.2 10.6 + - - -
44G LEU 3.1 1.0 - - - -
45G LEU* 1.3 80.7 - - - +
47G SER* 1.3 78.5 + - - +
48G ILE 3.4 5.2 + - - +
148G VAL* 4.1 0.3 - - - +
149G GLY* 3.7 24.9 + - - -
172G SER* 4.7 4.7 + - - -
30H ARG 5.8 0.7 - - - -
32H PHE* 4.0 6.5 - - - -
856I GLU* 3.5 31.1 + - - -
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Residues in contact with SER 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G ILE 3.0 8.6 + - - -
46G SER* 1.3 80.8 + - - +
48G ILE* 1.3 63.6 + - - +
49G PRO* 3.2 10.6 - - - +
148G VAL* 3.3 21.5 - - - +
217G ILE* 3.7 29.3 - - - +
29H GLU* 4.9 6.8 + - - +
32H PHE* 3.3 28.7 - - - -
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Residues in contact with ILE 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G ILE 4.1 2.5 - - - +
44G LEU* 3.1 37.0 - - + +
46G SER 3.4 5.2 - - - +
47G SER* 1.3 77.5 - - - +
49G PRO* 1.3 67.2 - - + +
148G VAL* 4.8 0.7 - - - -
149G GLY 4.5 1.7 + - - -
171G PHE* 4.5 1.6 - - - +
172G SER* 3.5 12.8 + - - -
173G PRO* 3.3 34.2 - - + +
174G VAL* 4.6 5.2 - - + -
205G VAL* 4.9 1.8 - - + -
210G ALA* 3.5 33.9 - - + +
213G GLN* 3.3 32.1 - - + +
214G ALA* 4.0 14.8 - - + +
217G ILE* 5.0 2.7 - - + -
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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