Contacts of the helix formed by residues 37 - 57 (chain C) in PDB entry 4IYM
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 37 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C THR* 3.4 9.8 + - - -
15C SER* 4.0 19.3 - - - -
17C ARG* 6.2 0.4 - - - +
35C LEU 3.4 2.8 + - - -
36C ALA* 1.3 78.7 - - - +
38C ASP* 1.3 65.4 + - - +
39C ALA* 3.4 7.4 + - - +
40C ASP* 3.1 31.4 + - - -
41C LEU* 3.3 18.0 + - - +
206C ALA* 5.8 1.4 - - - -
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Residues in contact with ASP 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C SER* 1.3 74.7 - - - +
39C ALA* 1.3 57.9 + - - +
41C LEU* 3.3 4.5 + - - +
42C ALA* 2.9 28.8 + - - +
205C GLY* 4.4 6.6 - - - +
209C ALA* 3.7 26.0 - - + +
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Residues in contact with ALA 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C THR* 4.5 8.1 - - - +
37C SER* 3.2 9.3 + - - +
38C ASP* 1.3 76.2 - - - +
40C ASP* 1.3 59.9 + - - +
42C ALA* 3.5 8.7 - - - +
43C ALA* 2.9 29.8 + - - +
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Residues in contact with ASP 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C HIS* 3.4 27.9 + - + +
6C ILE* 3.8 8.2 - - + +
12C ALA 4.4 1.7 - - - +
13C GLY* 3.8 2.4 - - - -
14C THR* 2.8 42.3 + - - +
15C SER 4.2 1.6 + - - -
35C LEU 4.4 0.3 - - - +
36C ALA* 3.5 10.9 - - + -
37C SER* 3.1 37.8 + - - +
39C ALA* 1.3 76.1 - - - +
41C LEU* 1.3 60.8 + - - +
43C ALA* 3.5 7.7 + - - +
44C ALA* 3.2 20.8 + - - +
200C VAL* 4.5 2.4 - - - +
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Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ALA* 5.3 0.7 - - + -
37C SER 3.3 8.2 + - - +
38C ASP 3.3 7.4 + - - +
40C ASP* 1.3 75.9 - - - +
42C ALA* 1.3 61.1 + - - +
44C ALA* 3.1 6.7 + - - +
45C VAL* 2.9 35.3 + - + +
169C ILE* 4.0 22.9 - - + -
200C VAL* 4.3 19.8 - - + +
206C ALA* 4.7 2.9 - - - +
209C ALA* 3.6 41.1 - - + +
210C ILE* 3.8 23.8 - - + +
213C HIS* 3.8 22.4 - - + -
216C ILE* 4.6 0.9 - - + -
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Residues in contact with ALA 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ASP 2.9 18.4 + - - +
39C ALA* 3.5 9.9 - - - +
41C LEU* 1.3 76.4 - - - +
43C ALA* 1.3 57.1 + - - +
45C VAL* 3.2 2.7 + - - +
46C GLU* 2.9 37.4 + - + +
213C HIS* 4.5 19.0 + - + +
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Residues in contact with ALA 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 4.2 13.9 - - + +
39C ALA 2.9 17.4 + - - +
40C ASP* 3.6 8.5 - - - +
41C LEU 3.3 0.2 - - - -
42C ALA* 1.3 75.2 - - - +
44C ALA* 1.3 56.7 + - - +
46C GLU* 3.8 6.1 - - - +
47C SER* 2.9 29.5 + - - -
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Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 4.0 16.3 - - + +
40C ASP 3.2 6.8 + - - +
41C LEU 3.1 7.0 + - - +
43C ALA* 1.3 76.7 - - - +
45C VAL* 1.3 57.6 + - - +
47C SER* 3.4 0.2 - - - -
48C ALA* 3.0 24.4 + - - +
169C ILE* 4.2 11.2 - - + +
198C ASN* 3.1 25.4 + - + +
200C VAL* 3.5 32.3 - - + -
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Residues in contact with VAL 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C LEU* 2.9 23.0 + - + +
42C ALA 3.7 6.3 - - - +
44C ALA* 1.3 74.9 - - - +
46C GLU* 1.3 57.0 + - - +
48C ALA* 3.1 5.1 + - - +
49C LYS* 2.8 41.5 + - + +
140C ILE* 4.5 6.1 - - + -
169C ILE* 3.4 25.6 - - + -
213C HIS* 3.4 43.7 - - + +
215C ASP* 3.9 15.5 - - + -
216C ILE* 4.0 10.8 - - + -
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Residues in contact with GLU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ALA* 2.9 23.4 + - + +
43C ALA* 3.8 6.1 - - - +
45C VAL* 1.3 75.0 - - - +
47C SER* 1.3 66.4 + - - +
49C LYS* 3.2 38.6 + - - +
50C ALA* 3.1 25.1 + - - +
213C HIS* 5.1 3.1 + - - -
215C ASP* 4.4 3.1 - - - +
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Residues in contact with SER 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C ILE* 3.7 10.5 - - - -
7C ASP* 2.5 35.3 + - - +
43C ALA 2.9 18.8 + - - -
44C ALA 3.4 7.0 - - - -
46C GLU* 1.3 77.4 - - - +
48C ALA* 1.3 60.1 - - - -
50C ALA* 3.5 5.1 + - - +
51C ALA* 3.3 22.2 + - - +
195C GLY* 3.3 5.8 - - - -
198C ASN* 3.1 16.8 + - - -
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Residues in contact with ALA 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ALA 3.0 14.5 + - - +
45C VAL* 3.1 8.9 + - - +
47C SER* 1.3 75.4 + - - +
49C LYS* 1.3 57.3 + - - +
51C ALA* 3.3 0.3 + - - +
52C GLN* 3.0 35.0 + - - +
140C ILE* 4.0 21.5 - - + -
167C ALA* 3.7 20.2 - - + +
168C PHE 5.3 0.7 - - - +
169C ILE* 4.7 5.4 - - + -
195C GLY 3.4 15.9 + - - +
198C ASN* 4.5 1.8 - - - +
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Residues in contact with LYS 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C VAL* 2.8 23.9 + - + +
46C GLU* 3.2 36.0 + - - +
48C ALA* 1.3 72.5 - - - +
50C ALA* 1.3 61.1 + - - +
52C GLN* 5.1 1.3 - - - -
53C PRO* 3.2 23.2 - - - +
140C ILE* 3.4 21.3 - - + -
215C ASP* 3.1 36.3 + - + +
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Residues in contact with ALA 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLU 3.1 15.7 + - - +
47C SER* 3.9 5.2 - - - +
49C LYS* 1.3 78.2 - - - +
51C ALA* 1.3 60.5 + - + +
53C PRO* 4.1 6.6 - - - +
54C LYS* 5.3 2.6 + - - +
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Residues in contact with ALA 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ASP* 5.4 0.7 - - - +
47C SER 3.3 12.9 + - - +
48C ALA 3.3 2.3 + - - +
49C LYS 3.2 0.4 - - - -
50C ALA* 1.3 81.5 - - + +
52C GLN* 1.3 64.8 + - - +
53C PRO 3.4 1.0 - - - -
54C LYS* 3.5 8.2 + - - +
55C TRP* 3.4 14.7 + - - +
193C PRO* 5.4 4.9 - - + +
194C ALA 3.3 26.2 - - - +
195C GLY 4.3 2.2 - - - -
196C ILE* 3.7 17.0 - - + +
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Residues in contact with GLN 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ALA 3.0 17.8 + - - +
49C LYS* 4.5 0.9 - - - +
51C ALA* 1.3 77.6 - - - +
53C PRO* 1.4 79.5 - - + +
55C TRP* 3.1 2.6 + - - +
56C ALA* 2.8 40.9 + - - +
137C PRO* 3.7 16.8 - - - +
139C GLY* 3.4 32.0 + - - +
140C ILE* 4.9 4.2 - - + +
165C GLY 3.1 23.7 + - - +
166C ASN 4.1 0.4 - - - -
167C ALA* 3.7 14.4 - - + +
196C ILE* 3.7 8.7 - - - -
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Residues in contact with PRO 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LYS 3.2 19.7 - - - +
50C ALA 4.1 5.2 - - - +
51C ALA 3.6 2.9 - - - -
52C GLN* 1.4 103.1 - - - +
54C LYS* 1.3 57.7 + - - +
56C ALA* 3.3 6.0 + - + +
57C ALA* 2.9 28.5 + - - +
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Residues in contact with LYS 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ALA 5.3 2.4 + - - +
51C ALA* 3.5 9.2 + - - +
52C GLN 3.4 0.4 - - - -
53C PRO* 1.3 77.6 - - - +
55C TRP* 1.3 61.7 + - - +
57C ALA* 3.3 9.7 + - + +
58C THR* 3.0 24.0 + - - -
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Residues in contact with TRP 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ALA 3.4 3.2 + - - +
52C GLN 3.1 7.0 + - - +
54C LYS* 1.3 77.2 - - - +
56C ALA* 1.3 62.7 + - - +
58C THR* 3.1 32.3 + - + -
62C ARG 5.2 0.2 - - - -
63C ARG* 3.6 51.7 - - + -
66C VAL* 4.0 18.6 - - + -
67C PHE* 4.9 2.7 - + - -
162C ILE* 2.9 46.5 + - + +
165C GLY* 3.7 15.0 - - - -
166C ASN 3.5 20.4 + - - -
191C GLY 5.3 0.2 - - - -
192C LEU* 3.7 11.7 - - + -
193C PRO* 3.6 35.6 - - + +
196C ILE* 3.6 28.0 - - + -
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Residues in contact with ALA 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLN* 2.8 32.4 + - - +
53C PRO* 3.7 6.5 - - + +
55C TRP* 1.3 73.3 - - - +
57C ALA* 1.3 59.6 + - - +
58C THR 3.3 6.5 + - - +
63C ARG* 4.0 7.4 + - - +
137C PRO* 3.9 13.9 - - + -
165C GLY* 3.5 24.3 + - - +
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Residues in contact with ALA 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLY 5.6 0.5 - - - +
127B PRO* 5.8 3.6 - - - +
53C PRO 2.9 15.9 + - - +
54C LYS* 3.6 11.0 - - + +
55C TRP 3.1 0.8 - - - -
56C ALA* 1.3 77.0 - - - +
58C THR* 1.3 61.7 + - - +
59C ASN* 3.6 2.3 + - - -
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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