Contacts of the strand formed by residues 28 - 37 (chain L) in PDB entry 4M7D
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 28 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53C ASN* 5.6 6.7 - - - +
27K LYS* 4.2 4.9 - - - +
29K ALA 4.7 10.5 + - - -
31K GLY* 4.3 9.8 - - - -
57K GLU* 2.2 39.4 + - - -
79K MET* 3.1 36.1 - - - +
23L VAL* 3.8 1.6 - - - +
24L LEU* 2.9 42.9 + - + +
26L SER* 3.1 14.4 + - - +
27L ASN* 1.3 80.3 - - - +
29L GLU* 1.3 66.7 + - - +
30L PHE* 4.0 9.0 - - + -
50L GLU* 3.1 20.5 + - + +
51L TRP 3.1 12.6 - - - +
52L LEU* 3.8 22.4 - - + +
64L VAL* 5.4 0.4 - - - +
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Residues in contact with GLU 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L LEU* 4.0 17.3 - - + +
22L ILE 3.2 11.7 - - - +
23L VAL* 3.7 24.7 - - + +
28L ARG* 1.3 79.1 - - - +
30L PHE* 1.3 70.3 + - - +
31L GLU 4.3 0.4 - - - -
49L VAL 3.7 0.4 - - - +
50L GLU* 3.5 1.0 - - - -
51L TRP* 2.9 46.2 + - + +
53L ILE* 3.4 30.0 - - + +
68M GLU* 4.5 1.9 - - - +
87M ARG* 2.9 33.9 + - - -
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Residues in contact with PHE 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79K MET* 3.1 37.0 - - + -
80K TYR* 3.7 15.3 - + - -
20L VAL 3.4 3.5 - - - +
21L LEU* 4.0 2.0 - - - -
22L ILE* 2.7 46.2 + - + +
24L LEU* 3.7 15.5 - - + -
28L ARG* 4.0 7.2 - - + -
29L GLU* 1.3 80.2 - - - +
31L GLU* 1.3 61.0 + - - +
32L GLY 4.0 0.2 + - - -
45L LEU* 3.7 17.3 - - + -
48L ALA* 4.4 6.7 - - + -
49L VAL 3.4 3.6 - - - +
50L GLU* 3.3 38.1 - - + -
67L HIS* 4.7 0.9 - - - -
71L MET* 3.7 22.4 - - + -
73L LEU* 3.8 19.5 - - + -
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Residues in contact with GLU 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L LYS* 4.0 28.2 - - + +
20L VAL 3.3 11.7 - - - +
21L LEU* 4.2 12.9 - - + +
29L GLU 4.3 0.2 - - - -
30L PHE* 1.3 74.4 - - - +
32L GLY* 1.3 61.6 + - - +
45L LEU* 5.4 0.2 - - - -
47L ASP 4.1 0.9 - - - +
48L ALA* 3.3 3.2 - - - -
49L VAL* 2.8 48.4 + - + +
51L TRP* 4.9 9.2 + - + +
85L GLY 3.1 30.6 - - - +
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Residues in contact with GLY 32 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L LYS* 4.4 10.3 - - - -
20L VAL* 2.9 35.6 + - - +
30L PHE 4.0 0.4 + - - -
31L GLU* 1.3 80.1 - - - +
33L THR* 1.3 64.0 + - - -
34L LEU 3.4 0.2 + - - -
45L LEU* 4.7 6.7 - - - +
46L GLU 3.7 10.3 - - - -
47L ASP 4.3 2.9 - - - -
48L ALA* 4.3 4.7 - - - -
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Residues in contact with THR 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L ASN* 3.9 20.0 - - - +
18L GLN 3.2 15.4 + - - +
19L LYS* 4.6 8.6 - - - +
32L GLY* 1.3 71.9 - - - -
34L LEU* 1.3 74.6 + - - +
35L VAL* 3.3 5.2 + - + +
45L LEU* 3.3 4.9 - - - -
46L GLU* 2.8 55.2 + - + +
47L ASP* 5.8 0.9 + - - +
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Residues in contact with LEU 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L ILE* 3.8 29.8 - - + +
15L THR* 3.3 34.3 - - + +
16L ILE* 3.7 12.9 - - + +
17L ASN* 2.8 31.5 + - - +
18L GLN 2.9 8.6 + - - +
20L VAL* 4.0 18.4 - - + -
32L GLY 3.4 2.8 + - - -
33L THR* 1.3 74.0 - - - +
35L VAL* 1.3 61.7 + - - +
36L GLY 3.8 17.0 - - - +
37L PHE* 4.8 0.9 - - + -
43L VAL* 4.3 17.0 - - + -
44L ILE 3.4 18.6 - - - +
45L LEU* 4.3 7.0 - - + -
81L LEU* 5.7 2.9 - - + -
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Residues in contact with VAL 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L ILE* 3.5 22.5 - - - +
17L ASN* 5.4 2.9 - - - -
33L THR* 3.8 7.6 - - + +
34L LEU* 1.3 74.7 - - - +
36L GLY* 1.3 61.2 + - - +
44L ILE* 3.0 26.3 + - + +
45L LEU 4.3 1.8 - - - -
46L GLU* 3.6 40.4 - - + +
70L ARG* 4.8 13.9 - - + +
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Residues in contact with GLY 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K VAL* 4.8 12.8 - - - -
16L ILE* 4.5 9.6 - - - -
34L LEU* 3.8 5.5 - - - +
35L VAL* 1.3 83.3 - - - +
37L PHE* 1.3 59.8 + - - +
43L VAL* 3.6 0.3 - - - -
44L ILE* 2.7 45.2 + - - +
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Residues in contact with PHE 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K VAL* 4.6 12.1 - - - +
12K THR* 5.5 1.3 - - - -
9L LEU* 3.7 46.2 - - + -
12L ILE* 3.5 35.7 - - + -
13L ASP* 3.8 28.5 - - + -
16L ILE* 4.0 14.6 - - + -
34L LEU* 4.8 2.5 - - + -
36L GLY* 1.3 77.4 - - - +
38L ASP* 1.3 78.8 + - - +
41L VAL* 4.9 5.6 - - + +
42L ASN 3.2 8.7 - - - +
43L VAL* 3.8 22.0 - - + -
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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