Contacts of the helix formed by residues 30 - 45 (chain A) in PDB entry 3A4I
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 GLY 30 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A SER* 2.9 17.8 + - - -
29A GLY* 1.3 79.3 - - - +
31A VAL* 1.3 62.8 + - - -
32A ASP 3.3 2.9 - - - -
33A SER* 3.7 2.7 + - - -
34A SER* 2.7 31.1 + - - -
185A ARG* 3.4 20.8 - - - +
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLY 4.0 0.4 + - - -
30A GLY* 1.3 72.4 - - - -
32A ASP* 1.3 71.7 + - - +
34A SER* 3.8 0.5 - - - -
35A THR* 2.7 38.1 + - - +
166A LYS* 3.7 22.9 - - - +
169A VAL* 4.2 9.2 - - + -
170A ARG* 4.2 19.1 - - + +
173A ALA* 3.8 26.9 - - + -
182A ILE* 3.9 20.4 - - + +
183A TYR* 4.0 16.2 - - + +
185A ARG* 4.0 9.2 - - + +
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Residues in contact with ASP 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLY 3.3 1.0 - - - -
31A VAL* 1.3 82.5 - - - +
33A SER* 1.3 63.6 + - - +
36A ALA* 3.0 20.3 + - - +
127A GLY* 3.4 19.8 - - - +
129A ILE* 3.9 25.2 + - - +
161A LEU* 3.3 16.1 - - - +
166A LYS* 3.0 34.0 + - - +
169A VAL* 3.7 11.1 - - - +
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Residues in contact with SER 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 3.6 7.7 - - - +
26A ALA 3.5 22.4 - - - -
27A LEU* 4.1 4.1 - - - +
28A SER* 2.9 36.4 + - - -
29A GLY 4.2 0.3 + - - -
30A GLY 3.7 3.7 + - - -
32A ASP* 1.3 78.7 - - - +
34A SER* 1.3 58.7 + - - +
36A ALA* 3.5 5.3 + - - -
37A ALA* 2.9 31.4 + - - +
127A GLY* 4.5 8.1 - - - -
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Residues in contact with SER 34 (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 LEU* 4.6 2.7 - - - +
29A GLY* 3.7 15.2 + - - -
30A GLY 2.7 24.7 + - - -
31A VAL 3.8 2.9 - - - -
33A SER* 1.3 78.4 + - - +
35A THR* 1.3 57.1 + - - +
37A ALA* 3.4 4.2 + - - +
38A VAL* 3.0 33.3 + - - +
70A PHE* 3.2 32.9 - - - -
178A LEU* 3.8 13.7 - - - -
182A ILE* 3.7 9.1 - - - +
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Residues in contact with THR 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 2.7 24.3 + - - +
32A ASP 3.8 3.4 - - - -
34A SER* 1.3 73.6 - - - +
36A ALA* 1.3 64.1 + - - +
38A VAL* 3.3 3.3 + - - +
39A LEU* 3.1 23.5 + - - +
161A LEU* 4.0 12.3 - - + -
169A VAL* 3.9 6.5 - - + +
172A LEU* 3.5 39.0 - - + -
173A ALA* 3.3 28.1 - - - +
176A LEU* 3.9 9.1 - - + +
178A LEU* 3.7 6.7 - - - +
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 4.0 12.6 - - + -
32A ASP 3.0 16.6 + - - +
33A SER 3.9 3.1 - - - +
35A THR* 1.3 76.5 - - - +
37A ALA* 1.3 57.4 + - - +
39A LEU* 3.5 4.7 + - - +
40A ALA* 3.0 29.1 + - - +
125A ILE* 4.2 3.9 - - + +
126A GLN 4.0 7.2 - - - +
127A GLY* 3.8 21.3 - - - -
160A PRO* 4.2 16.1 - - + +
161A LEU* 3.8 9.9 - - + +
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Residues in contact with ALA 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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25A ILE* 3.6 18.1 - - + +
27A LEU* 3.5 25.1 - - + -
33A SER 2.9 19.5 + - - +
34A SER* 3.6 4.9 - - - +
35A THR 3.2 0.2 - - - -
36A ALA* 1.3 73.3 - - - +
38A VAL* 1.3 60.5 + - - +
40A ALA 3.2 1.2 + - - -
41A HIS* 2.8 27.7 + - - +
48A LEU* 3.3 12.1 - - + +
70A PHE* 4.9 0.4 - - + -
76A MET* 3.8 17.0 - - + -
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER 3.0 16.9 + - - +
35A THR* 3.3 4.5 + - - +
37A ALA* 1.3 74.6 - - - +
39A LEU* 1.3 57.2 + - - +
41A HIS* 3.3 3.4 + - + +
42A LYS* 2.9 36.6 + - + +
70A PHE* 4.5 1.3 - - + -
74A PHE* 3.7 33.0 - - + -
76A MET* 3.6 20.9 - - + -
176A LEU* 3.8 33.0 - - + +
178A LEU* 3.8 20.0 - - + -
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Residues in contact with LEU 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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6A PHE* 4.3 13.9 - - + -
7A VAL* 4.1 40.8 - - + -
10A LYS* 4.5 8.5 - - + -
11A VAL* 4.0 11.7 - - + +
14A ILE* 4.1 9.3 - - + +
35A THR 3.1 13.2 + - - +
36A ALA* 3.6 6.7 - - - +
38A VAL* 1.3 77.2 - - - +
40A ALA* 1.3 63.4 + - - +
42A LYS* 3.3 7.1 + - - +
43A ALA* 3.0 21.7 + - - +
160A PRO* 3.8 19.1 - - + -
161A LEU* 3.8 29.6 - - + -
172A LEU* 4.4 2.0 - - + -
176A LEU* 4.1 13.5 - - + -
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Residues in contact with ALA 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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14A ILE* 4.0 17.8 - - + +
36A ALA 3.0 15.7 + - - +
37A ALA* 3.7 3.6 - - - +
39A LEU* 1.3 79.2 - - - +
41A HIS* 1.3 56.5 + - - +
43A ALA* 3.1 4.8 + - - +
44A ILE* 2.8 34.5 + - + +
48A LEU* 3.8 27.1 - - + -
125A ILE* 4.1 19.7 - - + -
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Residues in contact with HIS 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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37A ALA 2.8 18.0 + - - +
38A VAL* 3.6 5.2 - - + +
40A ALA* 1.3 73.7 - - - +
42A LYS* 1.3 64.8 + - + +
45A GLY* 2.8 59.3 + - - +
46A ASP* 4.3 4.5 - - - -
48A LEU* 3.6 11.8 - - + +
74A PHE* 3.3 28.0 + + + -
75A GLY 3.6 20.3 + - - -
76A MET* 3.9 30.9 - - + +
77A ASN 4.9 0.8 + - - -
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Residues in contact with LYS 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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7A VAL* 4.2 17.6 - - + +
11A VAL* 3.9 10.8 - - + -
15A ARG* 2.9 21.5 + - - -
38A VAL* 2.9 22.7 + - + +
39A LEU* 3.4 10.3 - - - +
41A HIS* 1.3 82.5 - - + +
43A ALA* 1.3 59.6 + - - +
45A GLY 4.8 0.2 + - - -
176A LEU* 3.9 33.0 - - + +
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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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11A VAL* 3.7 25.5 - - + +
14A ILE* 3.6 33.9 - - + -
15A ARG* 2.8 27.9 + - + +
39A LEU 3.0 13.3 + - - +
40A ALA 3.1 8.7 + - - +
42A LYS* 1.3 78.4 - - - +
44A ILE* 1.3 63.2 + - + +
45A GLY 3.8 0.2 - - - -
47A ARG* 4.9 1.0 + - - -
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Residues in contact with ILE 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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14A ILE* 4.3 7.0 - - + -
15A ARG* 4.4 10.3 - - - -
18A VAL* 3.9 29.2 - - + -
19A GLY 4.8 0.4 - - - +
23A ALA* 3.8 26.0 - - + -
40A ALA* 2.8 21.4 + - + +
43A ALA* 1.3 85.3 - - + +
45A GLY* 1.3 64.7 + - - +
46A ASP 3.4 0.7 + - - -
47A ARG* 3.1 56.0 + - + +
48A LEU* 3.6 27.8 - - + +
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Residues in contact with GLY 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 HIS* 2.8 40.9 + - - -
42A LYS 4.8 0.2 + - - -
43A ALA 3.8 0.4 - - - -
44A ILE* 1.3 75.5 - - - +
46A ASP* 1.3 57.9 + - - -
48A LEU* 2.9 28.8 + - - +
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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