Contacts of the helix formed by residues 35 - 47 (chain A) in PDB entry 1EFV
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 PRO 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.3 8.3 - - + +
34A ALA* 1.3 84.9 - - + +
36A ILE* 1.3 62.8 + - - +
38A LEU* 2.9 32.5 + - + +
39A ASN* 3.2 13.5 + - - +
175A ALA* 5.3 0.7 - - - +
211A GLU* 6.4 1.8 - - + -
214A GLY* 6.6 0.4 - - - -
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Residues in contact with ILE 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLU* 3.3 27.1 - - + +
34A ALA* 4.2 8.3 - - + -
35A PRO* 1.3 80.4 - - - +
37A THR* 1.3 65.6 + - - +
39A ASN* 3.2 10.5 + - - +
40A THR* 2.9 26.8 + - - +
111A GLY* 3.8 14.8 - - - +
112A ALA 3.7 28.7 - - - +
113A SER* 3.9 15.7 - - - +
168A VAL 4.3 4.0 - - - +
170A GLY* 4.1 22.2 - - - +
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Residues in contact with THR 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 4.4 11.2 - - + -
25A ILE 4.6 1.9 + - - +
26A ALA* 3.9 22.6 - - + -
27A GLU* 3.0 30.8 + - - +
33A LEU* 3.9 18.2 - - + -
34A ALA 3.0 15.9 + - - -
36A ILE* 1.3 80.3 - - - +
38A LEU* 1.3 55.2 + - - +
40A THR* 3.3 8.5 + - - -
41A ILE* 3.0 40.1 + - + +
53A CYS* 4.8 0.7 - - - -
67A LEU* 4.8 1.8 - - + -
111A GLY 5.6 1.3 - - - +
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 4.0 24.5 - - + -
35A PRO* 2.9 24.6 + - + +
37A THR* 1.3 75.8 - - - +
39A ASN* 1.3 64.4 + - - +
41A ILE* 3.4 12.7 + - + -
42A THR 3.4 6.6 + - - -
70A VAL* 4.1 26.2 - - + -
175A ALA* 3.8 20.0 - - + -
176A ALA* 3.1 37.1 + - + +
178A THR* 4.1 21.5 - - + -
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Residues in contact with ASN 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A PRO* 3.2 24.8 + - - +
36A ILE* 3.2 16.2 + - - +
38A LEU* 1.3 75.6 - - - +
40A THR* 1.3 63.8 + - - +
42A THR* 3.3 2.4 + - - -
43A ALA* 3.2 16.6 + - - +
168A VAL* 4.9 1.3 - - + -
169A ARG 5.2 0.2 - - - +
170A GLY* 3.4 34.2 + - - +
173A PHE* 2.8 33.6 - - + +
174A ASP 3.8 7.2 - - - -
175A ALA* 3.4 18.2 + - - +
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Residues in contact with THR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 4.0 10.8 - - + -
36A ILE* 2.9 15.3 + - - +
37A THR* 3.5 11.4 - - - -
39A ASN* 1.3 75.1 - - - +
41A ILE* 1.3 60.3 + - - +
43A ALA* 3.3 7.2 + - - +
44A ALA* 2.9 26.7 + - - +
109A CYS* 3.9 19.0 - - - -
110A ALA* 3.7 27.6 - - - -
111A GLY* 3.2 21.6 + - - -
168A VAL* 3.9 14.8 - - + +
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Residues in contact with ILE 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 4.5 15.5 - - + -
37A THR* 3.0 26.8 + - + +
38A LEU* 3.7 13.2 - - + +
39A ASN 3.3 0.2 - - - -
40A THR* 1.3 77.9 - - - +
42A THR* 1.3 61.3 + - - +
44A ALA* 3.2 7.8 + - - +
45A THR* 3.0 32.1 + - + +
51A VAL* 5.0 2.0 - - + -
53A CYS* 4.9 1.3 - - - -
67A LEU* 4.3 17.3 - - + -
70A VAL* 3.7 17.7 - - + -
71A ALA 4.1 9.4 - - - +
72A GLY 5.0 0.2 - - - -
73A ILE* 3.5 36.1 - - + -
176A ALA* 4.0 13.9 - - + -
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Residues in contact with THR 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU 3.4 0.8 + - - -
39A ASN 3.3 6.0 + - - -
40A THR 3.2 0.6 - - - -
41A ILE* 1.3 80.3 - - - +
43A ALA* 1.3 61.6 + - - +
45A THR* 2.8 23.5 + - - +
46A ARG* 3.0 36.2 - - + +
173A PHE* 4.3 2.7 - - + -
174A ASP* 2.6 40.2 + - + +
175A ALA 3.7 0.5 - - - -
176A ALA* 3.3 21.5 + - - +
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ASN 3.2 3.4 + - - +
40A THR 3.3 8.5 + - - +
42A THR* 1.3 77.7 - - - +
44A ALA* 1.3 63.8 + - - +
46A ARG* 3.1 10.6 + - - +
47A LEU* 3.7 1.2 + - - +
109A CYS* 6.1 0.2 - - - -
138A ILE* 3.1 26.2 - - + +
166A PHE* 5.2 2.0 - - + -
168A VAL* 3.8 28.5 - - + -
173A PHE* 3.7 37.2 - - + -
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR* 3.9 24.5 + - + -
24A VAL* 3.9 15.9 - - + -
40A THR 2.9 14.1 + - - +
41A ILE 3.5 8.7 - - - +
43A ALA* 1.3 77.2 - - - +
45A THR* 1.3 60.8 + - - +
47A LEU* 3.1 31.5 + - - +
48A GLY 4.2 1.2 + - - -
49A GLY 5.0 0.9 + - - -
51A VAL* 4.1 16.3 - - + +
109A CYS* 4.2 5.8 - - - -
166A PHE* 5.6 0.2 - - - -
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Residues in contact with THR 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ILE* 3.0 22.1 + - + +
42A THR* 2.8 25.9 + - - +
44A ALA* 1.3 75.0 - - - +
46A ARG* 1.3 63.3 + - - +
47A LEU 3.1 0.2 - - - -
48A GLY* 3.2 14.9 + - - +
49A GLY 4.9 2.1 + - - +
51A VAL* 4.1 19.7 - - + -
71A ALA 5.2 0.7 - - - +
72A GLY* 4.2 24.0 - - - +
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A THR* 3.0 33.0 - - - +
43A ALA* 3.1 15.2 + - - +
45A THR* 1.3 78.1 - - - +
47A LEU* 1.3 62.3 + - - +
48A GLY* 3.4 1.0 + - - -
137A ALA* 6.2 0.8 - - - +
138A ILE* 4.1 25.9 + - + +
141A PRO* 6.0 0.3 - - - +
172A SER 5.5 1.8 + - - -
173A PHE* 3.6 33.2 - - + +
174A ASP* 5.6 1.4 + - - +
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLN* 2.3 36.8 + - - +
22A THR* 3.5 27.8 - - + +
43A ALA 4.0 5.8 - - - +
44A ALA* 3.1 17.2 + - - +
46A ARG* 1.3 79.2 - - - +
48A GLY* 1.3 54.1 + - - +
49A GLY 4.5 1.1 - - - +
107A HIS* 3.8 30.1 - - + +
138A ILE* 4.0 23.6 - - + -
140A SER 6.0 0.2 - - - -
141A PRO* 3.7 34.9 - - + +
144A PHE* 4.3 7.2 - - + -
166A PHE* 4.0 14.8 - - + -
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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
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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