Contacts of the strand formed by residues 30 - 39 (chain B) in PDB entry 4EMG
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 ARG 30 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B LYS* 3.4 3.9 - - - +
26B LEU* 2.9 57.3 + - + +
27B ARG 4.5 4.9 + - - +
28B GLY 3.2 11.3 + - - +
29B ASP* 1.3 80.5 - - - +
31B GLU* 1.3 71.2 + - - +
32B LEU* 5.0 0.7 - - + -
52B GLU* 2.6 48.7 + - + +
53B ILE 3.7 1.3 - - - +
54B VAL* 3.4 25.6 - - + +
25C LYS* 3.3 39.0 - - - +
28C GLY 5.9 0.8 - - - +
86C ILE* 5.1 10.7 - - - +
87C LEU* 4.6 9.2 - - - -
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Residues in contact with GLU 31 (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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23B TYR* 2.7 41.6 + - + +
24B VAL 3.3 6.5 - - - +
25B LYS* 4.0 11.5 - - + +
26B LEU* 4.6 0.4 - - - +
29B ASP 5.7 0.4 - - - -
30B ARG* 1.3 78.5 - - - +
32B LEU* 1.3 75.2 + - - +
33B ASN* 5.4 0.7 - - - +
52B GLU* 3.4 0.9 - - - +
53B ILE* 2.9 50.2 + - + +
55B THR* 4.1 20.4 - - + +
73E LYS* 4.4 9.4 - - - +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B VAL 4.5 0.2 - - - -
23B TYR* 3.5 2.6 - - - -
24B VAL* 2.8 35.7 + - + +
26B LEU* 4.0 23.8 - - + -
30B ARG* 5.0 1.3 - - + -
31B GLU* 1.3 84.1 - - - +
33B ASN* 1.3 74.4 + - - +
47B LEU* 3.9 18.2 - - + -
50B ALA* 5.8 0.2 - - + -
51B GLU 3.2 6.5 - - - +
52B GLU* 3.7 28.3 - - + -
78B LEU* 3.9 17.3 - - + -
80B VAL* 3.4 43.1 - - + -
87C LEU* 4.5 3.8 - - + -
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Residues in contact with ASN 33 (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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21B ILE* 4.9 9.0 - - + +
22B VAL 3.3 8.2 - - - +
23B TYR* 3.7 27.4 + - - +
31B GLU* 5.3 0.6 - - - +
32B LEU* 1.3 80.1 + - - +
34B GLY* 1.3 58.1 + - - +
47B LEU* 4.7 2.7 - - - -
49B ASP 4.0 0.9 - - - +
50B ALA* 3.1 4.4 - - - +
51B GLU* 2.7 55.3 + - + +
53B ILE* 4.0 16.8 - - - +
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Residues in contact with GLY 34 (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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21B ILE* 3.2 12.2 - - - +
22B VAL* 2.8 33.4 + - - +
33B ASN* 1.3 76.4 - - - +
35B ARG* 1.3 63.1 + - - -
36B LEU 3.6 0.7 + - - -
47B LEU* 4.0 15.4 - - - +
48B GLY 3.5 10.8 - - - -
49B ASP 3.9 6.3 - - - -
50B ALA* 4.1 1.1 - - - -
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Residues in contact with ARG 35 (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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19B ASP* 2.9 48.6 + - - +
20B GLU* 3.4 6.7 + - - +
21B ILE* 3.7 32.0 - - + +
34B GLY* 1.3 71.0 - - - -
36B LEU* 1.3 59.7 + - - +
37B HIS* 3.0 34.7 + - + +
47B LEU* 3.4 2.6 - - - -
48B GLY 2.7 41.3 + - - +
49B ASP* 4.7 4.7 + - + +
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Residues in contact with LEU 36 (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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14B VAL* 3.3 40.8 - - + +
17B SER* 3.6 26.0 - - - +
18B LEU* 3.7 14.5 - - + +
19B ASP* 2.7 30.7 + - - -
20B GLU 2.9 11.3 + - - +
22B VAL* 4.3 14.1 - - + -
34B GLY 3.6 2.8 + - - -
35B ARG* 1.3 68.6 - - - +
37B HIS* 1.3 59.6 + - - +
38B ALA 3.6 25.4 - - - +
39B TYR* 4.4 1.8 - - + -
45B MSE 3.8 27.1 - - + -
46B VAL 3.9 1.3 - - - +
47B LEU* 4.0 10.3 - - + -
88B ILE* 6.0 0.9 - - + -
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Residues in contact with HIS 37 (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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18B LEU* 3.9 10.6 - - - +
19B ASP* 4.1 20.5 + - - +
35B ARG* 3.0 28.1 + - + -
36B LEU* 1.3 73.9 - - - +
38B ALA* 1.3 65.0 + - + +
46B VAL* 2.9 20.7 + - + +
48B GLY* 3.5 36.6 + - - -
77B MSE 3.7 23.4 - - + -
9C GLU* 4.6 5.2 - - - +
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Residues in contact with ALA 38 (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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18B LEU* 4.1 6.7 - - - +
36B LEU* 3.6 6.4 - - - +
37B HIS* 1.3 83.4 - - + +
39B TYR* 1.3 64.0 + - - +
45B MSE 3.1 4.0 - - - -
46B VAL* 2.9 32.9 + - + -
9C GLU* 3.3 31.6 - - + +
10C PRO* 3.8 18.6 - - + -
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Residues in contact with TYR 39 (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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11B LEU* 4.7 13.6 + - + +
14B VAL* 3.7 27.6 - - + -
15B ARG* 3.2 42.6 - - - +
18B LEU* 3.5 35.4 - - + +
36B LEU* 4.4 3.4 - - + -
38B ALA* 1.3 79.1 - - - +
40B ASP* 1.3 79.4 + - - +
43B LEU* 5.0 6.1 - - + -
44B ASN 3.0 13.7 - - - +
45B MSE 3.9 12.3 - - + -
9C GLU* 5.1 2.6 - - - +
10C PRO* 3.4 10.5 - - - +
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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