Contacts of the helix formed by residues 26 - 37 (chain G) in PDB entry 3REI
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 26 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18G SER* 3.4 8.7 - - - +
24G GLN 3.7 0.2 - - - -
25G PHE* 1.4 91.0 - - + +
27G VAL* 1.3 64.5 + - - +
28G GLY 3.2 2.2 - - - +
29G ARG* 3.2 27.7 + - + +
30G VAL* 3.0 26.3 + - + +
52G ALA* 4.7 0.4 - - - -
34H TYR* 4.5 9.2 - - + -
37H TYR* 3.6 49.1 - - + +
-43J A 6.5 0.4 - - - -
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Residues in contact with VAL 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G ARG* 4.0 36.6 - - + +
18G SER* 3.2 23.6 + - - +
21G ALA* 4.6 0.4 - - + -
23G LEU* 4.4 9.0 - - + -
25G PHE 3.2 3.3 + - - +
26G PRO* 1.3 70.6 - - - +
28G GLY* 1.3 63.2 + - - +
30G VAL* 3.8 2.4 - - - +
31G HIS* 2.9 23.1 + - - +
48G PRO* 3.9 5.0 - - + +
49G VAL* 3.7 41.3 - - + +
52G ALA* 4.0 22.2 - - + -
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Residues in contact with GLY 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G ARG* 4.0 11.6 + - - -
18G SER* 4.9 1.2 + - - -
26G PRO* 3.2 1.8 - - - +
27G VAL* 1.3 76.8 - - - +
29G ARG* 1.3 61.1 + - - +
31G HIS* 3.2 5.0 + - - +
32G ARG* 3.0 22.2 + - - +
-43J A 3.7 22.8 + - - -
-42J G 3.9 20.8 + - - -
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Residues in contact with ARG 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G PRO* 3.2 27.4 + - + +
28G GLY* 1.3 71.0 - - - +
30G VAL* 1.3 61.7 + - - +
32G ARG* 3.1 21.3 + - - +
33G LEU* 2.8 41.3 + - + +
30H ARG* 4.4 0.6 - - - +
32H GLU* 3.4 31.4 + - - +
33H SER 2.7 36.4 + - - +
34H TYR* 4.2 15.3 - - - +
37H TYR* 3.9 17.5 + - - -
47I G 3.0 21.8 + - - -
48I G 2.5 22.6 + - - -
-43J A 3.2 21.0 + - - +
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Residues in contact with VAL 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G PHE* 5.8 0.7 - - + -
26G PRO* 3.0 23.9 + - + +
27G VAL* 3.9 3.6 - - - +
29G ARG* 1.3 75.1 - - - +
31G HIS* 1.3 62.7 + - - +
33G LEU* 3.4 7.1 + - - +
34G LEU* 3.0 24.6 + - + +
48G PRO* 3.6 27.4 - - + +
51G LEU* 3.8 30.5 - - + -
52G ALA* 4.1 17.3 - - + +
55G LEU* 4.4 14.1 - - + -
34H TYR* 4.5 17.3 - - + +
67H PHE* 4.1 3.3 - - + -
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Residues in contact with HIS 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G ARG* 3.2 38.1 - - - +
27G VAL 2.9 14.1 + - - +
28G GLY 3.3 9.0 - - - +
30G VAL* 1.3 75.0 - - - +
32G ARG* 1.3 68.3 + - - +
34G LEU* 3.3 6.2 + - - +
35G ARG* 3.2 59.2 + - + +
43G VAL* 4.0 21.3 + - + +
44G GLY 4.6 2.6 + - - -
45G ALA* 5.1 3.8 - - - -
48G PRO* 3.6 21.7 - - + +
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Residues in contact with ARG 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G GLY 3.0 13.0 + - - +
29G ARG* 3.1 13.9 + - - +
31G HIS* 1.3 75.6 - - - +
33G LEU* 1.3 94.4 + - - +
35G ARG* 2.9 19.5 + - - +
36G LYS* 3.0 48.6 + - + +
32H GLU* 2.5 45.0 + - - -
-44J A 3.1 46.3 + - - -
-43J A 3.9 8.6 + - - +
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Residues in contact with LEU 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G ARG* 2.8 32.0 + - + +
30G VAL 3.8 1.8 - - - +
32G ARG* 1.3 101.0 - - - +
34G LEU* 1.3 57.1 + - - +
36G LYS* 3.8 4.9 - - + +
37G GLY* 2.9 27.9 + - - +
39G TYR* 3.9 3.3 - - - -
32H GLU* 5.0 0.4 - - - +
34H TYR* 3.3 30.1 - - + +
64H ASN* 5.5 2.2 - - - +
67H PHE* 3.6 24.9 - - + -
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Residues in contact with LEU 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30G VAL* 3.0 24.7 + - + +
31G HIS* 3.6 5.6 - - - +
32G ARG 3.2 0.2 - - - -
33G LEU* 1.3 77.4 - - - +
35G ARG* 1.3 63.0 + - - +
37G GLY* 3.3 2.4 + - - -
38G ASN 3.9 1.9 + - - -
39G TYR* 3.3 33.7 + - + +
40G ALA 5.3 1.4 + - - +
43G VAL* 4.2 27.9 - - + +
47G ALA* 4.6 6.1 - - + +
48G PRO* 4.1 29.6 - - + -
51G LEU* 4.3 11.4 - - + -
67H PHE* 4.1 9.9 - - + -
71H ALA* 4.0 29.2 - - + -
86H ILE* 5.0 8.7 - - + -
91H ILE* 4.9 8.5 - - + -
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Residues in contact with ARG 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C GLU* 4.9 6.8 - - - +
31G HIS* 3.2 46.1 + - + +
32G ARG* 2.9 10.6 + - - +
34G LEU* 1.3 78.2 - - - +
36G LYS* 1.3 70.3 + - + +
37G GLY 3.1 1.3 + - - -
38G ASN* 3.6 9.2 + - - -
39G TYR 5.1 0.2 + - - -
40G ALA 5.3 5.1 - - - +
41G GLU 4.9 3.4 + - - -
42G ARG* 4.8 2.0 - - - +
43G VAL* 4.0 16.5 + - + +
38I T 2.2 59.8 + - - +
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Residues in contact with LYS 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C GLU* 5.7 2.2 - - - -
79D HIS* 3.4 19.6 + - - -
32G ARG* 3.0 45.4 + - + +
33G LEU* 3.8 6.1 - - + +
35G ARG* 1.3 81.8 - - + +
37G GLY* 1.3 56.9 + - - +
38G ASN* 3.4 4.1 + - - +
-44J A 6.1 2.0 - - - -
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Residues in contact with GLY 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D HIS* 3.6 14.0 + - - -
33G LEU 2.9 18.5 + - - -
34G LEU 3.3 0.4 + - - -
35G ARG 3.1 1.2 - - - -
36G LYS* 1.3 78.0 - - - +
38G ASN* 1.3 71.5 + - - +
39G TYR* 3.3 29.9 + - - -
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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