Contacts of the strand formed by residues 41 - 47 (chain A) in PDB entry 4JE4
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 PHE 41 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.7 34.1 - + - -
31A ALA* 5.9 0.2 - - + -
32A ARG 3.5 15.0 - - - +
33A PRO* 3.9 10.1 - - + -
34A SER* 3.8 2.3 - - - +
39A GLY 4.1 5.6 - - - -
40A ASP* 1.3 83.9 - - - +
42A THR* 1.3 64.1 + - - +
55A LYS* 3.7 2.1 - - - -
56A ILE* 2.7 55.5 + - + +
58A ASN* 3.9 20.9 - - + -
63A TYR* 3.7 37.7 - + - -
74A LEU* 4.2 14.4 - - + -
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Residues in contact with THR 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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31A ALA* 3.4 4.3 - - - +
32A ARG* 2.8 80.0 + - - +
34A SER* 3.7 19.1 + - - -
41A PHE* 1.3 76.6 + - - +
43A LEU* 1.3 62.0 + - - +
44A SER* 4.0 2.5 - - - +
53A HIS* 3.8 20.2 - - + -
54A ILE 3.2 12.6 + - - +
55A LYS* 5.2 2.8 - - - +
56A ILE* 4.5 4.5 - - - -
84B TYR* 4.2 8.4 + - + +
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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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29A PHE* 4.2 12.3 - - + -
30A LEU 3.5 15.7 - - - +
31A ALA* 4.0 17.5 - - + -
42A THR* 1.3 70.7 - - - +
44A SER* 1.3 63.0 + - - +
45A VAL* 3.7 8.4 + - + +
52A THR 3.5 3.3 - - - +
54A ILE* 2.8 56.2 + - + +
56A ILE* 4.2 17.4 - - + +
65A LEU* 6.0 2.9 - - + -
77A LEU* 5.1 6.7 - - + -
78A VAL* 4.2 18.8 - - + -
81A TYR* 5.9 0.7 - - + -
88A LEU* 5.4 3.4 - - + -
98A LEU* 3.7 37.2 - - + -
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Residues in contact with SER 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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16A ALA* 4.3 4.0 - - - -
20A LEU* 3.5 17.5 - - - +
29A PHE* 3.2 4.5 - - - +
30A LEU* 3.0 44.5 + - - -
32A ARG* 2.8 31.5 + - - -
42A THR* 3.8 1.5 + - - +
43A LEU* 1.3 71.9 - - - +
45A VAL* 1.3 60.0 + - - +
51A VAL* 4.2 0.7 - - - -
52A THR 3.5 4.5 - - - -
53A HIS* 2.9 23.7 + - - -
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Residues in contact with VAL 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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20A LEU* 4.1 4.0 - - - +
28A SER 3.6 10.1 - - - +
29A PHE* 4.0 4.7 - - + -
43A LEU* 3.8 13.7 - - + +
44A SER* 1.3 79.0 - - - +
46A ARG* 1.3 70.7 + - - +
47A ARG* 3.6 4.6 + - + +
51A VAL* 3.3 2.2 - - - +
52A THR* 2.8 43.5 + - - +
54A ILE* 4.1 15.5 - - + -
96A ILE* 4.2 13.9 - - + -
97A GLU 3.5 25.8 - - - +
98A LEU* 3.6 26.5 - - + -
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Residues in contact with ARG 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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20A LEU* 3.0 44.8 + - + +
21A LEU* 3.6 35.6 + - + +
24A GLY 3.1 18.5 + - - -
25A VAL* 3.4 20.6 - - - +
26A ASP* 3.3 20.6 + - - +
27A GLY* 3.0 28.3 + - - -
28A SER 2.8 16.8 + - - +
45A VAL* 1.3 74.8 - - - +
47A ARG* 1.3 64.1 + - - +
49A GLY* 4.1 14.6 - - - -
50A ALA 3.2 12.3 - - - +
51A VAL* 4.4 2.2 - - + +
97A GLU 5.0 0.2 - - - +
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Residues in contact with ARG 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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26A ASP* 4.3 1.8 - - - -
27A GLY* 5.0 1.3 - - - +
45A VAL* 3.6 9.3 + - + +
46A ARG* 1.3 75.6 - - - +
48A ASN* 1.3 85.8 + - + +
49A GLY 3.3 1.3 - - - -
50A ALA* 2.7 26.0 + - - +
52A THR* 4.5 12.3 + - - +
90A GLU* 2.4 43.0 + - - -
94A ASP* 3.7 28.9 + - - +
95A VAL 3.2 23.7 + - - -
96A ILE* 4.0 18.5 - - + +
97A GLU* 4.4 14.4 - - + +
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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