Contacts of the helix formed by residues 45 - 59 (chain B) in PDB entry 6XWQ
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 ILE 45 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B PHE* 3.4 36.6 - - + -
41B VAL* 3.1 17.8 + - + +
44B TYR* 1.3 82.0 - - + +
46B LYS* 1.3 68.6 + - - +
47B PRO 3.2 2.0 - - - -
48B PHE* 2.8 35.8 + - + +
212B PHE* 4.6 13.2 - - + -
213B ALA* 3.6 33.7 - - + +
216B ALA* 4.9 6.7 - - + -
217B TYR* 5.3 1.6 - - + +
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Residues in contact with LYS 46 (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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41B VAL 3.0 10.9 + - - +
42B LYS* 3.2 45.3 - - + +
45B ILE* 1.3 78.2 - - - +
47B PRO* 1.3 65.6 - - + +
49B GLY* 2.9 6.0 + - - +
50B ASP* 2.9 40.8 + - + +
213B ALA 5.0 2.5 - - - -
214B LEU* 5.4 2.9 - - + +
217B TYR* 4.2 41.3 - - + +
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Residues in contact with PRO 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A VAL* 4.5 22.7 - - + -
137A LEU* 3.4 31.8 - - + +
42B LYS 3.9 3.6 - - - +
43B THR 3.7 16.8 - - - +
44B TYR 3.3 20.9 - - - +
46B LYS* 1.3 97.0 - - + +
48B PHE* 1.3 60.7 + - + +
50B ASP* 4.2 2.9 - - + -
51B LEU* 2.9 30.1 + - - +
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Residues in contact with PHE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 6.4 0.7 - - + -
44B TYR 5.1 7.2 - - - -
45B ILE* 2.8 31.8 + - + +
47B PRO* 1.3 77.1 - - + +
49B GLY* 1.3 57.3 + - - +
51B LEU* 3.3 10.8 + - + +
52B PHE* 2.9 26.0 + - - +
206B TYR* 3.6 21.4 + + - +
209B ILE* 4.7 29.6 - - + +
210B GLY* 4.4 2.0 - - - -
212B PHE* 6.5 0.4 - + - -
213B ALA* 3.6 12.8 - - + -
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Residues in contact with GLY 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LYS 2.9 7.4 + - - -
48B PHE* 1.3 78.9 - - - +
50B ASP* 1.3 57.0 + - - +
52B PHE* 3.2 3.3 + - - +
53B VAL* 2.9 32.2 + - - +
210B GLY 3.8 10.5 - - - -
213B ALA* 3.4 9.1 - - - +
214B LEU* 3.7 30.3 - - - +
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Residues in contact with ASP 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLN* 4.8 7.1 + - - +
137A LEU* 3.8 17.9 - - + +
46B LYS* 2.9 31.3 + - + +
47B PRO* 3.8 7.9 - - + +
49B GLY* 1.3 75.2 - - - +
51B LEU* 1.3 57.7 + - - +
53B VAL* 3.3 11.6 + - - +
54B ARG* 2.9 47.3 + - - +
214B LEU* 4.4 2.1 - - - +
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 6.3 2.0 - - + -
137A LEU* 4.1 23.9 - - + +
140A VAL* 3.6 36.1 - - + -
47B PRO 2.9 18.5 + - - +
48B PHE* 3.6 10.5 - - + +
50B ASP* 1.3 75.6 - - - +
52B PHE* 1.3 60.0 + - - +
54B ARG* 3.3 5.5 + - - +
55B LEU* 2.9 44.6 + - + +
206B TYR* 3.2 26.0 - - + +
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Residues in contact with PHE 52 (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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48B PHE 2.9 14.2 + - - +
49B GLY 3.2 6.0 + - - +
51B LEU* 1.3 78.3 - - - +
53B VAL* 1.3 57.8 + - + +
55B LEU* 3.3 3.8 + - - +
56B LEU* 2.9 45.8 + - + +
203B VAL* 3.8 20.6 - - + -
204B MET* 5.2 0.2 - - + -
206B TYR* 4.0 15.0 - + + -
207B ALA* 3.5 34.8 - - + -
210B GLY* 3.9 26.2 - - - -
211B VAL* 4.4 16.4 - - + -
214B LEU* 4.3 15.5 - - + -
277B THR* 3.2 33.2 - - - -
359B PRO* 5.7 1.3 - - + -
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLY 2.9 19.6 + - - +
50B ASP* 3.3 12.8 + - - +
52B PHE* 1.3 78.7 - - + +
54B ARG* 1.3 58.8 + - + +
56B LEU* 3.2 6.9 + - - +
57B LYS* 2.9 57.3 + - + +
214B LEU* 3.7 26.9 - - + -
278B ARG* 5.9 0.4 - - - +
359B PRO* 4.1 28.2 - - + +
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Residues in contact with ARG 54 (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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134A GLN* 4.9 7.0 - - - +
137A LEU* 3.1 31.0 + - - -
138A ASN* 4.0 27.8 + - - +
140A VAL* 3.2 32.6 + - + +
141A PRO* 3.7 5.9 - - - +
142A THR* 3.0 33.7 + - - +
155A PRO* 6.3 0.2 - - - +
50B ASP* 2.9 35.3 + - - +
51B LEU* 3.7 2.0 - - - +
53B VAL* 1.3 77.3 - - + +
55B LEU* 1.3 59.1 + - - +
57B LYS* 3.2 13.3 + - + +
58B MET* 2.9 27.4 + - - +
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Residues in contact with LEU 55 (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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140A VAL* 3.8 24.5 - - + -
158A PHE* 4.1 9.2 - - + -
51B LEU* 2.9 29.2 + - + +
52B PHE* 3.4 8.1 - - - +
54B ARG* 1.3 76.1 - - - +
56B LEU* 1.3 61.7 + - - +
58B MET* 3.1 41.8 + - + +
59B LEU* 3.5 15.5 - - - +
203B VAL* 4.5 22.7 - - + -
206B TYR* 4.0 32.8 - - + -
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Residues in contact with LEU 56 (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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52B PHE* 2.9 50.3 + - + +
53B VAL* 3.2 5.1 + - - +
55B LEU* 1.3 75.9 - - - +
57B LYS* 1.3 59.8 + - - +
59B LEU* 3.9 22.8 + - + +
60B VAL* 4.3 1.2 - - - +
200B VAL* 5.5 2.0 - - + -
203B VAL* 4.2 17.0 - - + -
204B MET* 4.5 3.6 - - + -
277B THR* 3.5 5.8 - - - +
279B SER* 3.1 30.7 - - - +
281B SER 5.6 0.7 - - - +
282B GLY* 3.9 30.0 + - - +
357B GLY 4.8 2.6 - - - +
358B VAL* 3.6 11.9 - - - +
359B PRO* 4.2 14.1 - - + -
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Residues in contact with LYS 57 (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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142A THR* 2.8 41.4 - - + +
143A ASN* 4.6 1.9 - - - +
53B VAL* 2.9 41.5 + - + +
54B ARG* 3.2 9.2 + - + +
56B LEU* 1.3 75.4 - - - +
58B MET* 1.3 65.2 + - - +
59B LEU 3.1 2.2 - - - -
60B VAL* 3.3 20.0 - - + +
61B MET 4.8 0.2 + - - -
358B VAL* 3.6 37.9 - - + -
359B PRO 4.4 6.7 + - - -
364B ILE* 5.6 8.6 - - - +
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Residues in contact with MET 58 (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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141A PRO* 3.2 37.5 - - + +
142A THR 3.4 9.4 + - - -
144A PRO* 3.4 19.5 - - + +
158A PHE* 4.1 14.1 - - + -
159A PHE* 3.9 28.9 - - + -
162A ILE* 4.7 7.0 - - + -
54B ARG 2.9 8.0 + - - +
55B LEU* 3.1 36.3 + - + +
57B LYS* 1.3 78.8 - - - +
59B LEU* 1.3 79.7 + - + +
62B PRO* 3.5 13.3 - - - +
199B ILE* 4.7 7.4 - - + -
203B VAL* 5.4 1.3 - - + -
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Residues in contact with LEU 59 (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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159A PHE* 5.3 0.7 - - + -
55B LEU 3.5 17.8 + - - +
56B LEU* 3.9 14.1 + - + +
57B LYS 3.1 1.0 - - - -
58B MET* 1.3 98.3 - - + +
60B VAL* 1.3 58.3 + - - +
61B MET 3.9 0.4 - - - -
62B PRO* 4.5 3.6 - - - -
63B ILE* 3.1 35.8 - - + +
196B MET* 4.1 18.2 - - + -
199B ILE* 3.6 32.3 - - + -
200B VAL* 3.5 23.8 - - + -
203B VAL* 3.8 18.6 - - + -
281B SER* 3.6 10.8 + - - +
282B GLY* 6.3 0.4 - - - -
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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