Contacts of the helix formed by residues 8 - 22 (chain B) in PDB entry 5E1M
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 8 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B ILE* 3.4 2.8 - - - -
7B GLU* 1.3 80.2 - - + +
9B GLU* 1.3 59.0 + - - +
10B LYS* 3.3 12.6 + - - +
11B GLN* 3.0 48.0 + - + +
12B PHE* 2.9 24.9 + - - +
311B UNX 2.9 15.9 - - - -
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Residues in contact with GLU 9 (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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6B ILE* 3.9 13.1 - - + +
7B GLU 4.3 0.4 - - - -
8B ASP* 1.3 70.8 + - - +
10B LYS* 1.3 67.9 + - - +
12B PHE* 3.2 2.4 + - + +
13B TYR* 3.1 38.7 + - + -
142B THR* 3.6 16.4 - - + +
145B HIS* 3.4 20.9 - - - -
309B UNX 2.8 23.0 - - - -
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Residues in contact with LYS 10 (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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8B ASP* 3.3 9.1 + - - +
9B GLU* 1.3 79.1 - - - +
11B GLN* 1.3 59.3 + - + +
13B TYR* 3.4 6.1 + - - +
14B SER* 2.8 33.4 + - - +
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Residues in contact with GLN 11 (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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8B ASP* 3.0 41.7 + - + +
10B LYS* 1.3 74.6 - - + +
12B PHE* 1.3 66.8 + - - +
14B SER* 3.4 10.8 - - - +
15B LYS* 2.9 58.8 + - - +
311B UNX 4.4 3.6 - - - -
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Residues in contact with PHE 12 (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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6B ILE* 3.7 43.5 - - + -
8B ASP 2.9 14.0 + - - +
9B GLU 3.2 7.8 + - - +
11B GLN* 1.3 76.6 - - - +
13B TYR* 1.3 73.5 - + - +
15B LYS* 5.6 0.2 - - - -
16B ALA 3.5 4.7 + - - -
139B GLY 3.4 22.0 - - - -
140B HIS 3.3 22.4 - - - -
141B LEU 4.1 11.2 - - - -
142B THR* 4.2 3.8 - - + -
176B LEU* 4.2 9.4 - - + -
181B SER* 2.7 49.9 + - - -
182B SER* 3.9 9.4 - - - -
183B VAL* 4.2 7.0 - - + -
311B UNX 4.0 4.8 - - - -
316B UNX 3.4 17.0 - - - -
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Residues in contact with TYR 13 (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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9B GLU* 3.1 40.1 + - + -
10B LYS* 3.8 7.4 - - - +
12B PHE* 1.3 80.0 - + - +
14B SER* 1.3 66.0 + - - +
16B ALA* 3.3 3.5 + - - +
17B LYS* 3.1 22.5 + - - +
92B ILE* 5.5 2.8 - - + +
120B GLN* 3.4 39.3 - - + +
140B HIS 3.1 26.5 - - - -
141B LEU* 3.7 2.1 - - - -
142B THR* 3.2 23.8 + - + -
145B HIS* 2.6 41.2 + + - +
310B UNX 3.8 6.1 - - - -
316B UNX 3.8 5.2 - - - -
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Residues in contact with SER 14 (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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10B LYS* 2.8 26.6 + - - +
11B GLN* 3.4 14.9 - - - +
13B TYR* 1.3 74.0 - - - +
15B LYS* 1.3 67.8 + - - +
17B LYS* 3.2 8.2 + - - +
18B THR* 3.1 26.5 + - - -
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Residues in contact with LYS 15 (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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43A ASN* 5.4 1.6 + - - -
11B GLN* 2.9 50.7 + - + +
14B SER* 1.3 80.7 + - - +
16B ALA* 1.3 56.5 + - - +
18B THR* 3.4 7.1 + - - -
19B TYR* 2.8 29.1 + - - +
178B ASP 5.6 5.6 - - - +
181B SER* 3.7 17.7 - - - +
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Residues in contact with ALA 16 (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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12B PHE 3.5 8.7 + - - +
13B TYR 3.3 1.9 + - - +
14B SER 3.2 0.4 - - - -
15B LYS* 1.3 79.6 - - - +
17B LYS* 1.3 62.0 + - - +
19B TYR* 3.2 0.9 + - - +
20B TRP* 3.1 31.3 + - + -
140B HIS* 3.4 19.5 - - + +
180B ASP 3.6 11.2 - - - -
181B SER* 3.6 5.1 - - - +
301B SAH 5.7 1.3 - - - -
310B UNX 3.5 9.0 - - - -
316B UNX 3.2 26.5 - - - -
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Residues in contact with LYS 17 (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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13B TYR 3.1 12.7 + - - +
14B SER* 3.2 10.7 + - - +
16B ALA* 1.3 78.1 - - - +
18B THR* 1.3 63.0 + - - +
20B TRP* 3.4 1.8 + - - +
21B LYS* 3.0 29.3 + - + +
92B ILE* 4.3 49.0 + - + +
93B THR* 4.9 2.9 + - - +
301B SAH 6.2 0.2 - - - -
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Residues in contact with THR 18 (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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43A ASN* 3.8 15.9 - - - +
46A ARG* 4.0 7.6 - - - +
14B SER* 3.1 14.8 + - - -
15B LYS* 3.6 9.8 - - - -
17B LYS* 1.3 75.5 - - - +
19B TYR* 1.3 68.7 + - - +
21B LYS* 3.3 17.5 + - + +
22B GLN* 3.4 32.8 + - - +
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Residues in contact with TYR 19 (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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36A HIS 4.4 0.5 + - - -
39A SER* 2.7 41.3 + - - -
40A ILE* 3.9 28.0 + - + +
43A ASN* 4.1 10.1 - - - +
315A UNX 3.9 3.5 - - - -
15B LYS 2.8 20.7 + - - +
16B ALA 3.2 6.7 + - - +
18B THR* 1.3 77.0 - - - +
20B TRP* 1.3 79.8 + + - +
22B GLN* 3.2 5.9 + - - +
23B ILE* 3.6 26.4 - - + +
179B VAL* 3.4 27.0 - - + +
180B ASP* 3.7 30.3 - - + +
312B UNX 2.6 30.0 - - - -
320B UNX 4.3 2.2 - - - -
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Residues in contact with TRP 20 (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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16B ALA 3.1 25.9 + - - +
17B LYS* 4.2 1.8 - - - +
19B TYR* 1.3 87.4 - + - +
21B LYS* 1.3 65.6 + - - +
22B GLN 3.0 2.5 - - - -
23B ILE* 3.1 27.9 + - + +
29B GLY 3.7 10.1 - - - -
30B MET* 4.0 5.6 - - - -
92B ILE* 5.4 0.7 - - + -
93B THR* 3.6 20.1 - - - +
96B PHE* 3.3 36.1 - + + -
140B HIS* 3.0 28.4 + + - -
180B ASP* 4.9 2.0 - - - +
301B SAH 3.4 54.0 - + + +
320B UNX 3.2 26.9 - - - -
1E PRO* 4.0 11.7 - - + -
101E UNX 3.6 18.2 - - - -
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Residues in contact with LYS 21 (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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78A ARG* 3.3 35.8 + - - +
17B LYS* 3.0 23.2 + - + +
18B THR* 3.5 11.7 - - + +
20B TRP* 1.3 76.2 - - - +
22B GLN* 1.3 62.8 + - + +
23B ILE 3.7 2.6 + - - +
93B THR* 4.4 14.1 + - + +
95B ASP* 4.9 8.9 - - - +
96B PHE* 5.8 0.5 - - - -
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Residues in contact with GLN 22 (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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38A SER* 4.0 11.8 + - - -
39A SER* 3.0 46.2 + - - +
42A ILE* 3.8 12.4 - - + +
43A ASN* 2.8 25.8 + - - -
46A ARG* 3.0 34.5 + - - -
78A ARG* 4.2 30.3 + - + +
18B THR* 3.4 19.4 + - - +
19B TYR 3.2 2.4 + - - -
20B TRP 3.0 1.2 - - - -
21B LYS* 1.3 82.8 - - + +
23B ILE* 1.3 57.9 + - - +
24B PRO 4.0 0.5 - - - -
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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