Contacts of the strand formed by residues 36 - 46 (chain B) in PDB entry 4Y1L
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 MET 36 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B LEU* 5.8 0.9 - - - +
28B PRO* 3.7 30.5 - - + +
29B THR 3.1 25.6 - - - +
30B LYS* 3.9 17.0 - - + -
31B ASN* 3.9 5.7 - - - +
35B THR* 1.3 76.2 - - - +
37B ASN* 1.3 62.2 + - - +
38B LEU* 3.5 8.8 + - + -
14C GLU* 4.6 19.1 - - + +
17C SER* 3.2 59.1 + - - +
18C VAL* 4.0 14.4 - - + +
21C ALA* 3.0 25.1 - - + +
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Residues in contact with ASN 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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28B PRO* 3.5 6.8 - - - +
29B THR* 2.9 32.2 + - - +
30B LYS 5.3 0.2 - - - -
31B ASN* 3.8 27.0 + - - +
35B THR 4.3 0.2 + - - -
36B MET* 1.3 72.0 - - - +
38B LEU* 1.3 56.9 + - - +
39B MET* 3.2 23.7 + - - +
40B ASN* 2.9 42.8 + - - +
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Residues in contact with LEU 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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6B LEU* 3.3 45.7 - - + +
9B LEU* 3.0 40.3 - - + +
10B ALA* 4.2 13.0 - - + +
13B ARG* 5.0 3.4 - - + -
28B PRO* 4.0 22.9 - - + -
36B MET* 3.5 17.1 + - + +
37B ASN* 1.3 70.0 + - - +
39B MET* 1.3 60.8 + - - +
40B ASN 3.2 2.7 - - - -
41B TRP* 2.4 28.8 + - + +
18C VAL* 4.3 18.8 - - + -
21C ALA* 4.6 6.5 - - + -
22C ILE* 4.4 6.7 - - + -
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Residues in contact with MET 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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2B SER* 4.3 7.6 - - - +
5B ALA* 4.0 14.6 - - + -
6B LEU* 4.1 22.7 - - + -
9B LEU* 3.5 23.3 - - - -
37B ASN* 3.2 10.9 + - - +
38B LEU* 1.3 77.5 - - - +
40B ASN* 1.3 57.4 + - + +
63B LEU* 3.4 3.8 - - - +
64B PHE* 2.8 44.8 + - - +
65B LYS 3.4 26.0 - - - +
66B ASP* 3.3 30.1 - - - +
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Residues in contact with ASN 40 (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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29B THR* 3.0 21.3 + - - +
37B ASN* 2.9 44.2 + - - +
39B MET* 1.3 80.8 - - - +
41B TRP* 1.3 67.8 + - - +
61B ARG* 3.2 43.3 + - - +
62B MET 3.4 3.3 - - - +
63B LEU* 3.8 19.8 - - + +
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Residues in contact with TRP 41 (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 LEU* 3.8 22.4 - - + +
12B GLU* 4.1 2.2 - - + -
13B ARG* 4.0 27.8 - - + -
16B TRP* 5.3 3.8 - + + -
26B ALA* 3.8 44.4 - - + -
27B VAL 3.4 3.6 - - - +
28B PRO* 3.6 24.9 - - + +
29B THR* 4.3 0.4 - - - -
38B LEU* 2.4 37.5 + - + +
40B ASN* 1.3 84.8 + - - +
42B GLU* 1.3 60.9 + - - +
43B CYS* 3.8 13.7 - - - -
61B ARG* 3.3 9.9 - - - +
62B MET* 2.9 36.0 + - + -
64B PHE* 3.5 14.5 - + - -
109B ILE* 3.6 33.4 - - + -
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Residues in contact with GLU 42 (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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25B VAL* 4.4 3.6 - - - +
26B ALA* 4.0 0.2 - - - -
27B VAL* 2.7 39.7 + - + +
29B THR* 3.6 15.9 - - + +
41B TRP* 1.3 71.4 - - - +
43B CYS* 1.3 59.8 + - - +
60B LEU 4.1 3.1 - - - -
61B ARG* 3.0 44.7 + - + +
78B GLU* 5.3 0.9 - - - +
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Residues in contact with CYS 43 (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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25B VAL* 3.1 13.0 - - - +
26B ALA* 4.0 16.4 - - - -
41B TRP* 3.8 24.5 - - - -
42B GLU* 1.3 80.2 - - - +
44B ALA* 1.3 61.7 + - - +
59B LYS* 3.5 6.4 - - - +
60B LEU* 2.9 48.1 + - + +
62B MET* 4.1 24.5 - - - -
109B ILE* 5.4 0.2 - - - -
113B LEU* 4.3 9.9 - - + -
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Residues in contact with ALA 44 (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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24B PHE* 3.6 8.0 - - - -
25B VAL* 2.9 52.0 + - + +
43B CYS* 1.3 75.1 - - - +
45B ILE* 1.3 65.7 + - - +
57B LEU* 3.8 24.0 - - + -
58B PHE 3.5 8.3 - - - +
59B LYS* 4.3 10.5 - - + -
60B LEU* 4.2 0.4 - - - -
113B LEU* 5.1 0.7 - - - +
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Residues in contact with ILE 45 (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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24B PHE* 4.0 6.3 - - + -
44B ALA* 1.3 78.7 - - - +
46B PRO* 1.3 79.5 - - + +
57B LEU* 3.9 2.0 - - - -
58B PHE* 2.9 45.5 + - + +
60B LEU* 3.8 18.8 - - + -
77B PHE* 4.6 5.2 - - + -
113B LEU* 3.8 35.2 - - + +
116B ILE* 3.7 29.6 - - + -
117B GLN* 3.6 26.0 - - + -
120B LEU* 4.1 10.1 - - + -
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Residues in contact with PRO 46 (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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22B PHE 3.9 4.7 - - - +
23B GLY* 3.2 33.4 - - - +
24B PHE* 3.6 36.6 - - + -
45B ILE* 1.3 85.8 - - - +
47B GLY* 1.3 63.5 + - - +
56B GLY 3.4 8.5 - - - +
57B LEU* 3.9 7.6 - - + -
58B PHE* 4.8 0.4 - - - -
117B GLN* 2.8 34.7 + - - +
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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