Contacts of the helix formed by residues 40 - 55 (chain B) in PDB entry 3C3P
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 ASP 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B ILE* 3.3 6.0 + - - +
39B VAL* 1.3 79.1 - - - +
41B ARG* 1.3 59.9 + - - +
42B GLN* 3.3 13.4 + - - +
43B THR* 2.8 44.7 + - - -
44B GLY* 3.0 23.9 + - - -
72B TRP* 5.2 0.2 + - - -
199B GLY* 3.7 19.2 - - - -
215B PEG 5.4 1.9 - - - +
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Residues in contact with ARG 41 (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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17B LEU* 3.9 30.4 - - + +
18B PRO* 2.8 38.8 + - - +
19B GLU 3.7 2.4 + - - -
20B ALA* 3.4 34.4 - - - +
24B VAL* 4.9 6.3 - - + +
28B GLU* 4.0 23.9 + - - +
39B VAL 3.8 0.6 + - - -
40B ASP* 1.3 72.9 - - - +
42B GLN* 1.3 65.7 + - + +
44B GLY* 3.4 0.7 + - - +
45B ARG* 3.0 41.4 + - - +
72B TRP* 4.4 22.7 - - + -
180C GLU* 3.7 14.5 + - - -
222C EDO 4.6 7.5 + - - -
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Residues in contact with GLN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A THR* 3.9 18.9 + - - +
195A ILE 5.3 3.5 + - - +
13B LEU* 3.2 36.4 + - + +
14B ASP* 3.1 27.3 + - - +
17B LEU* 3.6 24.2 - - + +
40B ASP* 3.3 13.2 + - - +
41B ARG* 1.3 77.3 - - + +
43B THR* 1.3 61.4 + - - +
45B ARG* 3.5 6.8 + - - +
46B LEU* 3.1 21.5 + - - +
198B VAL* 3.9 8.1 - - + +
215B PEG 3.6 28.7 - - - +
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Residues in contact with THR 43 (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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39B VAL* 3.6 20.2 - - + -
40B ASP* 2.8 25.3 + - - -
42B GLN* 1.3 74.1 - - - +
44B GLY* 1.3 64.9 + - - +
46B LEU* 3.1 6.5 + - + +
47B LEU* 2.9 29.6 + - + +
158B VAL* 3.8 28.7 - - + -
198B VAL* 4.0 10.3 + - - +
199B GLY* 3.7 19.2 + - - -
200B ASN 4.6 1.7 + - - -
202B VAL* 3.9 13.9 - - + +
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Residues in contact with GLY 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 3.4 6.8 - - - +
40B ASP 3.0 12.5 + - - -
41B ARG 3.4 1.3 + - - -
43B THR* 1.3 76.4 - - - +
45B ARG* 1.3 60.4 + - - +
47B LEU* 3.1 9.2 + - - +
48B TYR 3.0 18.9 + - - -
72B TRP* 3.3 44.1 - - - -
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Residues in contact with ARG 45 (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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192A PHE* 3.4 39.8 - - + -
193A THR* 2.9 30.5 + - - +
194A THR* 4.5 10.9 + - - +
218A EDO 3.2 29.3 + - - -
17B LEU* 3.6 27.0 - - - +
18B PRO* 3.7 24.3 - - - +
41B ARG* 3.0 32.0 + - - +
42B GLN* 3.8 8.3 + - - +
44B GLY* 1.3 75.2 - - - +
46B LEU* 1.3 61.6 + - - +
48B TYR* 3.3 1.0 + - - +
49B LEU* 3.0 18.7 + - - +
72B TRP* 3.9 19.8 - - + -
216B PEG 5.0 5.1 - - - -
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A THR* 4.6 7.4 + - + +
196A VAL* 4.2 20.9 - - + -
204A LEU* 5.0 2.5 - - + -
42B GLN 3.1 12.4 + - - +
43B THR* 3.1 10.4 + - - +
45B ARG* 1.3 73.1 - - - +
47B LEU* 1.3 68.7 + - + +
49B LEU* 3.2 18.3 + - + +
50B LEU* 2.9 58.9 + - + +
196B VAL* 3.9 14.8 - - + -
198B VAL* 3.4 33.7 - - + -
202B VAL* 4.4 12.3 - - + -
204B LEU* 5.3 2.2 - - + -
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Residues in contact with LEU 47 (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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39B VAL* 4.4 10.8 - - + -
43B THR* 2.9 27.4 + - + +
44B GLY* 3.1 15.0 + - - +
46B LEU* 1.3 77.3 - - + +
48B TYR* 1.3 63.0 + - - +
50B LEU* 3.5 6.8 + - + +
51B ALA* 3.0 24.9 + - - +
69B ALA* 4.4 14.1 - - + -
72B TRP* 4.3 8.3 - - + -
73B PHE* 3.9 33.6 - - + -
130B PHE* 3.8 23.3 - - + -
156B ILE* 3.7 32.3 - - + -
158B VAL* 4.8 0.2 - - + -
202B VAL* 5.4 2.2 - - + -
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Residues in contact with TYR 48 (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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192A PHE* 3.7 42.8 - + + -
206A TYR* 5.6 0.2 - + - -
208A LEU* 4.2 1.8 - - + +
44B GLY 3.0 12.3 + - - +
45B ARG 3.5 7.2 - - - +
47B LEU* 1.3 76.7 - - - +
49B LEU* 1.3 64.7 + - - +
51B ALA* 3.3 3.5 + - - +
52B ARG* 2.8 65.6 + - + +
72B TRP* 3.7 35.3 - + + +
75B ARG* 3.5 35.2 + - + -
76B ALA* 3.7 11.0 - - + +
214B PEG 5.0 0.5 - - - -
216B PEG 3.6 31.7 - - - -
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 4.5 4.7 - - + -
192A PHE* 4.2 15.7 - - + +
194A THR* 3.6 20.0 - - + +
204A LEU* 3.5 38.1 - - + +
206A TYR* 3.6 32.1 - - + +
45B ARG 3.0 13.0 + - - +
46B LEU* 3.4 14.8 - - + +
48B TYR* 1.3 81.4 - - - +
50B LEU* 1.3 66.7 - - + +
52B ARG* 3.1 4.2 + - - +
53B ILE* 3.0 45.6 + - + +
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Residues in contact with LEU 50 (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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49A LEU* 5.2 1.1 - - + -
50A LEU* 4.1 19.3 - - + -
53A ILE* 3.8 22.9 - - + +
46B LEU* 2.9 47.1 + - + +
47B LEU* 3.8 4.9 - - + +
49B LEU* 1.3 79.7 - - + +
51B ALA* 1.3 56.1 + - - +
53B ILE* 3.3 7.0 + - + +
54B LYS* 2.8 31.6 + - - +
128B ILE* 4.9 1.8 - - + -
154B LEU* 4.6 7.6 - - + -
156B ILE* 4.1 21.8 - - + -
204B LEU* 3.6 38.8 - - + -
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Residues in contact with ALA 51 (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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47B LEU 3.0 18.1 + - - +
50B LEU* 1.3 74.4 - - - +
52B ARG* 1.3 64.5 + - - +
55B GLN* 2.9 20.6 + - - -
56B PRO* 3.1 15.1 - - + +
59B VAL* 5.6 0.2 - - + -
73B PHE* 4.0 20.4 - - + +
76B ALA* 3.6 23.7 - - + +
77B ILE* 5.1 0.9 - - + -
128B ILE* 4.0 18.1 - - + +
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Residues in contact with ARG 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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152A ASN* 4.0 1.4 + - - +
206A TYR* 3.5 54.4 + - + -
208A LEU* 3.6 17.6 - - - +
209A SER* 3.2 29.1 + - - +
48B TYR* 2.8 70.8 + - + +
49B LEU* 3.1 8.0 + - - +
51B ALA* 1.3 77.6 - - - +
53B ILE* 1.3 62.7 + - - +
55B GLN* 3.4 18.4 + - - +
76B ALA* 3.4 23.6 - - + +
214B PEG 3.8 32.3 + - - -
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Residues in contact with ILE 53 (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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50A LEU* 4.3 18.2 - - + +
53A ILE* 3.4 25.8 - - + +
54A LYS* 3.5 43.6 - - + +
154A LEU* 4.0 24.0 - - + -
206A TYR* 4.1 21.5 - - + -
49B LEU* 3.0 39.5 + - + +
50B LEU* 3.6 7.0 - - + +
52B ARG* 1.3 78.7 - - - +
54B LYS* 1.3 62.3 + - - +
55B GLN* 3.5 5.9 + - - +
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Residues in contact with LYS 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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53A ILE* 3.8 28.9 - - + +
50B LEU 2.8 19.8 + - - +
51B ALA 4.0 2.5 - - - +
53B ILE* 1.3 78.5 - - - +
55B GLN* 1.3 68.2 + - - +
56B PRO* 4.1 10.4 - - + +
127B ASP* 3.4 35.1 + - - +
128B ILE* 4.2 17.0 - - + -
151B LYS 5.0 0.8 + - - -
152B ASN 3.1 20.6 + - - -
153B ALA* 4.5 0.2 - - - +
154B LEU* 3.9 17.3 - - + +
212B EDO 2.7 43.5 + - - +
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Residues in contact with GLN 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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152A ASN* 4.0 21.0 + - - +
206A TYR* 4.5 3.4 + - - -
51B ALA 2.9 11.7 + - - -
52B ARG 3.4 17.4 + - - +
53B ILE 4.0 5.1 + - - +
54B LYS* 1.3 80.7 - - - +
56B PRO* 1.3 69.1 - - - +
57B GLN* 3.0 19.0 + - - +
214B PEG 5.7 8.2 + - - +
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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
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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