Contacts of the strand formed by residues 41 - 51 (chain A) in PDB entry 4RLC
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 VAL 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A PHE* 3.4 4.6 - - - -
37A LEU* 2.7 52.3 + - + -
38A THR* 2.9 25.7 + - + +
40A ASP* 1.4 78.8 - - + +
42A GLU* 1.3 62.2 + - - +
43A LEU* 4.8 4.3 - - + -
73A ALA* 5.3 4.5 - - + -
74A ILE 3.3 10.5 - - - +
75A TYR* 4.2 19.5 - - + -
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Residues in contact with GLU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLU* 3.6 13.6 - - - +
9A GLU* 5.7 0.7 - - - +
32A SER* 5.4 0.5 + - - -
34A GLY* 3.3 21.7 + - - -
35A TYR 3.3 15.0 - - - +
36A PHE* 3.8 19.7 - - + -
40A ASP 3.9 0.2 + - - -
41A VAL* 1.3 75.8 - - - +
43A LEU* 1.3 72.8 + - - +
44A ALA* 4.1 9.6 - - - +
73A ALA* 3.4 4.0 - - - +
74A ILE* 2.8 47.9 + - + +
76A HIS* 3.2 20.0 - - + -
120A LYS* 3.2 23.7 + - - -
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLY* 3.1 2.6 - - - -
35A TYR* 2.8 35.8 + - + +
37A LEU* 3.4 42.2 - - + -
41A VAL* 4.8 2.9 - - + -
42A GLU* 1.3 78.9 - - - +
44A ALA* 1.3 58.7 + - - +
71A LEU* 5.2 7.4 - - + -
72A ASP 3.5 3.6 - - - +
73A ALA* 4.1 20.9 - - + -
207A C8E 3.9 19.5 - - + +
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A SER* 3.7 18.8 - - - +
33A ILE 3.3 7.0 - - - +
34A GLY* 4.1 5.4 - - - -
42A GLU* 4.1 7.0 - - - +
43A LEU* 1.3 76.3 - - - +
45A LEU* 1.3 59.4 + - - +
46A SER* 4.2 3.3 + - - +
70A SER 3.6 1.2 - - - +
71A LEU* 3.3 10.4 - - - +
72A ASP* 2.9 35.9 + - + +
74A ILE* 3.8 20.2 - - + -
207A C8E 4.5 0.4 - - - -
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A SER* 3.2 2.6 + - - -
33A ILE* 2.9 33.4 + - + +
44A ALA* 1.3 73.1 - - - +
46A SER* 1.3 60.2 + - - +
69A THR* 4.3 9.0 - - + -
70A SER 3.3 14.4 - - - +
71A LEU* 4.4 9.2 - - + -
202A C8E 3.6 37.5 - - + +
203A C8E 3.9 54.1 - - + +
207A C8E 4.0 20.5 - - + +
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Residues in contact with SER 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 4.2 14.3 - - - -
31A GLY 3.3 9.0 - - - -
32A SER* 3.4 19.4 + - - -
44A ALA* 4.8 3.5 + - - +
45A LEU* 1.3 73.7 + - - +
47A TYR* 1.3 61.8 + - - +
68A LEU 4.4 1.1 - - - -
69A THR* 3.3 9.5 - - - +
70A SER* 2.9 45.4 + - - -
72A ASP* 4.7 5.3 + - - -
202A C8E 4.4 3.3 - - - +
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Residues in contact with TYR 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 3.8 4.7 - - - -
30A GLY* 3.2 2.6 - - - -
31A GLY 2.9 30.7 + - - +
46A SER* 1.3 75.7 - - - +
48A GLY* 1.3 60.9 + - - +
49A GLU* 3.1 36.5 + - + -
67A ASN* 3.2 43.8 + - + +
68A LEU 3.4 3.4 - - - -
69A THR* 3.5 21.1 - - - -
202A C8E 3.5 44.8 - - + +
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Residues in contact with GLY 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A PHE* 4.2 5.1 - - - -
28A LEU* 3.6 15.5 - - - -
29A TYR 3.2 12.1 - - - -
30A GLY* 3.9 2.5 - - - -
47A TYR* 1.3 78.1 - - - +
49A GLU* 1.3 64.1 + - - -
67A ASN* 3.1 7.6 - - - +
68A LEU 2.9 33.8 + - - +
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Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 3.5 5.3 - - - -
29A TYR* 2.8 32.6 + - + +
47A TYR* 3.1 37.4 + - + +
48A GLY* 1.3 74.6 - - - +
50A TYR* 1.3 62.8 + - - +
51A HIS* 3.6 28.7 + - + +
66A GLY 3.4 11.4 - - - +
67A ASN* 4.2 0.4 - - + -
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Residues in contact with TYR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TYR* 3.1 36.9 + + - -
26A ALA* 5.0 6.1 - - + -
27A ASP 3.3 13.0 - - - +
28A LEU* 3.8 20.9 - - + -
49A GLU* 1.3 72.9 - - - +
51A HIS* 1.3 73.9 + - - +
53A VAL 5.5 8.7 - - - +
64A VAL* 4.7 12.9 - - + +
65A HIS* 4.9 5.6 - - - -
66A GLY* 3.0 41.3 + - - +
67A ASN* 3.7 23.3 - - - -
68A LEU* 3.8 18.1 - - + +
95A GLN* 2.9 31.5 + - + -
97A ILE* 4.5 10.5 - - + -
136A GLN* 4.0 0.9 + - - -
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Residues in contact with HIS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ALA* 4.1 0.5 - - - -
27A ASP* 2.9 32.5 + - - +
29A TYR* 3.5 42.0 - + + -
49A GLU* 3.6 32.2 + - + +
50A TYR* 1.3 89.2 + - - +
52A ASP* 1.3 71.2 + - - +
53A VAL 3.5 4.7 + - - -
64A VAL 5.6 2.7 - - - -
65A HIS* 5.8 7.9 - + - -
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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