Contacts of the helix formed by residues 38 - 58 (chain L) in PDB entry 4ZZ7
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 38 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L GLU* 2.4 39.3 + - - -
17L THR* 5.0 2.2 - - - -
18L ARG* 5.1 3.1 - - - -
36L LEU 3.4 2.4 + - - -
37L ALA* 1.3 76.6 - - - +
39L THR* 1.3 67.1 + - - +
40L LYS* 3.1 8.8 + - - +
41L THR* 3.0 11.4 + - - -
42L VAL* 3.1 11.4 + - - +
206L GLU* 3.1 26.2 - - - -
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Residues in contact with THR 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L SER* 1.3 75.3 - - - +
40L LYS* 1.3 65.5 + - - +
42L VAL* 3.4 1.4 + - - +
43L GLU* 3.0 36.5 + - - +
206L GLU* 3.2 35.0 + - + +
209L ASP* 6.2 0.4 - - + -
210L ALA* 3.9 23.3 - - + +
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Residues in contact with LYS 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L GLU* 5.9 2.2 - - + -
38L SER* 3.1 7.9 + - - +
39L THR* 1.3 82.5 + - - +
41L THR* 1.3 63.9 + - - +
43L GLU* 3.4 15.7 + - - +
44L GLN* 3.2 42.6 + - + +
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Residues in contact with THR 41 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6L HIS* 3.8 21.3 - - + +
8L ILE* 3.7 17.4 - - + +
13L VAL* 5.5 1.8 - - + -
14L THR 6.3 0.2 - - - -
15L GLU* 2.7 38.5 + - + +
37L ALA* 3.6 20.2 - - + -
38L SER 3.0 6.1 + - - -
40L LYS* 1.3 76.2 - - - +
42L VAL* 1.3 65.1 + - - +
44L GLN* 3.3 19.8 + - - +
45L ALA* 3.3 15.2 + - - +
201L VAL* 4.4 1.1 - - + +
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Residues in contact with VAL 42 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L ALA* 4.3 5.8 - - + -
38L SER 3.1 13.2 + - - +
39L THR 3.8 2.0 - - - +
41L THR* 1.3 74.7 - - - +
43L GLU* 1.3 64.9 + - + +
45L ALA* 3.0 5.0 + - - +
46L ILE* 2.9 37.1 + - + +
170L VAL* 5.3 0.7 - - + -
201L VAL* 4.1 21.1 - - + -
207L ALA* 3.9 33.4 - - + +
210L ALA* 3.5 26.2 - - + -
211L LEU* 3.9 20.0 - - + -
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Residues in contact with GLU 43 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L THR* 3.0 28.1 + - - +
40L LYS* 3.5 16.7 - - - +
42L VAL* 1.3 76.1 - - + +
44L GLN* 1.3 57.2 + - - +
46L ILE* 4.3 5.2 - - + -
47L SER* 2.9 33.0 + - - +
210L ALA* 5.9 2.7 - - + +
214L ASP* 3.8 20.1 - - - +
216L ARG* 3.6 12.3 + - - +
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Residues in contact with GLN 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L ILE* 3.9 18.8 - - + +
13L VAL* 5.3 4.3 - - - +
40L LYS* 3.2 45.1 + - + +
41L THR* 3.5 19.8 + - - +
42L VAL 3.2 1.0 - - - -
43L GLU* 1.3 72.8 - - - +
45L ALA* 1.3 62.1 + - - +
47L SER* 3.4 6.6 + - - -
48L ALA* 2.9 29.3 + - - +
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Residues in contact with ALA 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L ILE* 3.8 19.0 - - + +
41L THR 3.3 3.1 + - - +
42L VAL 3.0 9.1 + - - +
44L GLN* 1.3 78.2 - - - +
46L ILE* 1.3 59.8 + - - +
48L ALA* 3.3 3.5 + - - +
49L ALA* 2.9 28.9 + - - +
170L VAL* 4.0 16.8 - - + -
199L ASN* 3.8 11.3 + - + -
201L VAL* 3.6 29.2 - - + -
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Residues in contact with ILE 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42L VAL* 2.9 37.2 + - + +
43L GLU* 3.9 6.1 - - + +
45L ALA* 1.3 76.6 - - - +
47L SER* 1.3 55.2 - - - +
49L ALA* 3.2 3.0 + - - +
50L GLN* 2.8 28.2 + - - +
141L VAL* 4.4 9.4 - - + -
170L VAL* 4.3 11.4 - - + -
210L ALA 4.5 2.9 - - - +
211L LEU* 4.1 11.7 - - + -
214L ASP* 3.7 29.2 - - + +
216L ARG* 3.5 42.6 - - + +
217L VAL* 3.9 18.4 - - + -
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Residues in contact with SER 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L GLU* 2.9 18.4 + - - +
44L GLN* 3.8 7.4 - - - -
46L ILE* 1.3 76.1 - - - +
48L ALA* 1.3 57.1 + - - +
50L GLN* 3.9 2.8 - - - +
51L HIS* 3.0 30.5 + - - +
216L ARG* 2.6 28.7 + - - +
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Residues in contact with ALA 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L ILE* 4.2 3.8 - - + -
9L ASN* 3.8 31.0 - - + +
44L GLN 2.9 18.3 + - - +
45L ALA 3.4 5.4 - - - +
47L SER* 1.3 74.7 - - - +
49L ALA* 1.3 65.0 + - - +
51L HIS* 3.1 7.0 + - - +
52L ALA* 3.0 24.8 + - - +
196L GLY* 4.0 4.0 - - - -
199L ASN* 3.6 16.2 - - - +
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Residues in contact with ALA 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45L ALA 2.9 17.3 + - - +
46L ILE 3.5 4.0 - - - +
48L ALA* 1.3 75.8 - - - +
50L GLN* 1.3 62.6 + - - +
52L ALA 3.3 0.2 + - - -
53L PHE* 3.3 18.2 + - - +
141L VAL* 3.7 26.2 - - + -
168L CYS* 3.3 22.8 - - + +
169L PHE 4.4 1.3 - - - +
170L VAL* 4.1 4.7 - - + -
196L GLY 3.3 12.2 + - - -
199L ASN* 3.6 12.8 - - - +
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Residues in contact with GLN 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46L ILE 2.8 20.3 + - - +
47L SER* 4.0 5.6 - - - +
49L ALA* 1.3 74.1 - - - +
51L HIS* 1.3 62.1 + - - +
53L PHE* 3.5 22.0 + - - +
54L PRO* 3.3 22.6 - - - +
140L GLY* 5.3 1.4 - - - -
141L VAL* 3.4 23.4 + - + +
216L ARG* 4.0 35.8 - - + +
218L LYS* 5.6 2.1 - - - +
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Residues in contact with HIS 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L ASN* 5.5 5.8 - - - -
47L SER 3.0 19.1 + - - +
48L ALA* 3.1 7.2 + - - +
50L GLN* 1.3 77.2 - - - +
52L ALA* 1.3 62.1 + - + +
53L PHE 3.3 1.1 + - - -
54L PRO* 3.5 11.5 - - - +
55L THR* 5.5 0.9 + - - +
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Residues in contact with ALA 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L ASN* 5.6 0.7 - - - +
48L ALA 3.0 15.5 + - - +
49L ALA 3.9 3.1 - - - +
50L GLN 3.3 0.2 - - - -
51L HIS* 1.3 77.9 - - + +
53L PHE* 1.3 61.3 + - - +
54L PRO* 3.7 0.7 - - - -
55L THR* 3.7 9.8 + - - -
56L TRP* 3.4 21.8 + - - +
168L CYS* 3.8 1.6 - - - -
194L PRO* 5.7 1.5 - - + +
195L ASP 3.4 25.4 - - - +
196L GLY* 3.7 13.0 - - - -
197L VAL* 3.9 10.1 - - + +
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Residues in contact with PHE 53 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430I GLN* 6.2 1.3 - - - -
49L ALA 3.3 14.8 + - - +
50L GLN* 3.6 21.1 - - - +
52L ALA* 1.3 75.2 - - - +
54L PRO* 1.4 70.3 - - + +
56L TRP 3.1 2.1 + - - -
57L ARG* 2.6 65.9 + - + +
138L PRO* 3.7 10.8 - - + -
139L MET 4.0 4.0 - - - -
140L GLY* 3.3 46.7 - - - -
166L GLY 3.1 28.3 - - - -
168L CYS* 3.5 13.7 - - + -
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Residues in contact with PRO 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50L GLN* 3.3 18.2 - - - +
51L HIS* 3.5 11.0 - - - +
52L ALA 3.8 0.2 - - - -
53L PHE* 1.4 99.5 - - + +
55L THR* 1.3 64.9 + - + +
57L ARG* 3.3 20.0 - - + +
58L ASN* 3.4 15.7 + - - -
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Residues in contact with THR 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51L HIS 5.5 0.6 + - - +
52L ALA* 3.7 10.1 + - - -
53L PHE 3.4 0.6 - - - -
54L PRO* 1.3 79.4 - - + +
56L TRP* 1.3 59.8 + - - +
58L ASN* 3.4 6.5 + - - +
59L THR* 2.8 28.9 + - - -
194L PRO* 6.0 3.1 - - - +
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Residues in contact with TRP 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L ALA 3.4 17.4 + - - +
53L PHE* 3.1 3.9 + - - +
55L THR* 1.3 77.2 + - - +
57L ARG* 1.3 66.0 + - - +
59L THR* 3.2 38.5 + - + -
63L LYS* 5.3 1.8 - - + -
64L ARG* 3.2 54.2 + - + +
67L VAL* 4.2 11.0 - - + -
163L ILE* 2.8 42.6 + - + +
164L VAL* 5.0 0.4 - - - -
166L GLY 3.7 11.9 - - - -
167L ASN 3.4 21.5 + - - -
168L CYS* 4.5 1.6 - - - -
193L LEU* 3.8 13.7 - - + -
194L PRO* 3.7 32.1 - - + -
197L VAL* 4.0 16.6 - - + -
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Residues in contact with ARG 57 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427I ASP* 3.2 39.2 + - - -
428I ASN* 3.4 21.9 - - - +
430I GLN* 4.1 19.8 - - - +
452I TRP* 5.3 1.2 - - - -
124K ARG* 3.1 34.3 + - - +
53L PHE* 2.6 49.9 + - + +
54L PRO* 3.3 13.7 + - - +
56L TRP* 1.3 72.3 - - - +
58L ASN* 1.3 65.9 + - - +
64L ARG* 3.2 11.6 + - - -
137L GLN* 3.5 29.9 + - - +
138L PRO* 3.8 18.6 + - + +
166L GLY 4.0 9.5 + - - -
473L LYS* 6.3 0.2 - - - +
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Residues in contact with ASN 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423I ARG* 6.0 1.6 - - - -
427I ASP* 3.9 4.6 - - - +
428I ASN* 4.0 15.3 - - - +
124K ARG* 3.0 20.1 + - - -
125K ASN* 3.3 20.0 + - - +
128K PRO* 5.2 5.0 - - - +
129K GLY 5.5 0.5 + - - -
54L PRO 3.4 15.2 + - - +
55L THR* 3.4 6.0 + - - +
56L TRP 3.3 0.4 - - - -
57L ARG* 1.3 91.5 + - - +
59L THR* 1.3 65.4 + - - +
60L PRO* 3.5 5.2 - - - +
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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
------------------------------------------------------------
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