Contacts of the strand formed by residues 45 - 52 (chain A) in PDB entry 4LEO
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 LEU 45 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 3.9 18.2 - - + -
38A ARG 3.9 1.3 - - - -
39A GLN* 3.8 33.7 - - + +
44A GLY* 1.3 73.2 - - - -
46A GLU* 1.3 62.2 + - - +
95A TYR* 4.7 6.5 - - + -
110A TRP* 4.7 2.2 - - + -
42B TYR* 5.2 1.8 - - + -
44B GLN* 4.5 0.2 - - - +
50B PRO* 3.7 33.0 - - + -
93B TYR* 3.6 38.1 - - + -
104B PHE* 3.4 49.3 - - + +
105B GLY 4.6 2.1 + - - +
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Residues in contact with GLU 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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37A VAL* 3.2 7.3 - - - +
38A ARG* 3.0 77.6 + - + +
44A GLY 4.9 1.8 - - - +
45A LEU* 1.3 76.4 - - - +
47A TRP* 1.3 73.7 + - - +
48A MET* 3.5 2.8 + - - +
61A ASN* 4.9 7.1 + - - +
63A LYS* 5.9 6.2 - - - +
64A LEU* 4.4 11.1 - - - +
104B PHE* 4.1 1.6 - - - +
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Residues in contact with TRP 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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35A SER* 3.3 27.1 + - - -
36A TRP 4.1 5.8 - - - -
37A VAL* 4.3 5.6 - - + -
46A GLU* 1.3 77.9 - - - +
48A MET* 1.3 60.8 + - - +
49A GLY* 3.3 20.7 - - - -
50A TRP* 3.5 17.0 - + - -
59A SER* 3.5 15.5 - - - -
60A TYR 4.1 1.3 - - - -
61A ASN* 3.0 40.6 + - + -
99A HIS* 5.8 0.2 - - - -
107A LEU* 5.8 1.6 - - + -
95B GLN* 5.0 5.4 - - - -
100B TYR* 3.6 37.0 - + - -
101B PRO* 3.0 36.8 - - + +
102B TYR* 3.4 33.8 - + + +
103B THR* 5.6 0.7 - - - -
104B PHE* 3.7 20.8 - - + -
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Residues in contact with MET 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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36A TRP* 2.9 41.6 + - + +
37A VAL 3.6 11.7 - - - +
38A ARG* 3.6 27.8 - - + +
46A GLU* 4.0 2.5 - - - +
47A TRP* 1.3 77.5 - - - +
49A GLY* 1.3 60.2 + - - +
60A TYR* 3.8 4.0 - - - +
61A ASN* 2.9 27.1 + - - +
64A LEU* 4.1 21.4 - - + +
68A VAL* 5.3 4.8 - - + +
70A MET* 4.1 10.5 - - + +
81A MET* 3.7 15.5 - - + -
83A LEU* 5.0 2.2 - - - -
94A TYR* 3.5 43.7 - - + -
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Residues in contact with GLY 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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35A SER* 3.3 3.5 + - - -
36A TRP 2.8 26.7 + - - -
47A TRP* 3.3 16.0 + - - -
48A MET* 1.3 81.7 - - - +
50A TRP* 1.3 60.6 + - - -
59A SER 3.1 15.5 - - - -
60A TYR* 4.3 0.4 - - - -
70A MET* 3.5 16.3 - - - +
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Residues in contact with TRP 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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33A TYR* 3.5 28.9 - + + -
34A ILE 3.3 10.5 - - - +
35A SER* 3.1 16.4 - - - +
47A TRP* 3.5 27.4 - + - -
49A GLY* 1.3 72.3 - - - -
51A ILE* 1.3 69.8 + - - +
57A SER 3.5 13.0 - - - -
58A PRO* 3.3 5.5 - - - +
59A SER* 3.0 45.8 + - - -
70A MET* 3.9 5.2 - - - +
99A HIS* 3.7 19.5 - + + +
102B TYR* 3.1 31.5 + + - -
102C LEU* 4.2 2.7 - - + -
104C TYR* 3.0 27.6 - + - -
132C LYS* 3.7 39.7 - - + +
159C ASP* 5.1 0.4 - - - -
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Residues in contact with ILE 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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33A TYR* 3.4 2.3 - - - -
34A ILE* 2.8 52.2 + - + +
36A TRP* 5.2 3.4 - - - +
50A TRP* 1.3 84.7 - - - +
52A TYR* 1.3 67.5 + - - +
53A ALA 3.6 0.9 + - - -
56A GLY* 3.6 32.5 - - - +
57A SER 3.6 7.4 - - - +
58A PRO* 4.3 2.9 - - + -
70A MET* 3.5 44.6 - - + +
71A THR* 3.8 17.7 - - - +
72A THR* 3.9 15.5 - - - +
79A ALA* 5.5 1.3 - - + -
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Residues in contact with TYR 52 (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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30A ARG 3.7 5.9 + - - -
31A SER* 3.7 10.4 + - - -
32A SER 3.5 20.4 - - - -
33A TYR* 3.5 28.5 - + + -
50A TRP* 4.1 1.0 - - - -
51A ILE* 1.3 71.8 - - - +
53A ALA* 1.3 58.3 + - - +
54A GLY* 3.2 28.4 + - - -
55A THR* 3.5 17.5 - - + +
56A GLY* 2.8 34.3 + - - -
57A SER 3.1 14.2 + - - +
102A TYR* 2.7 42.1 + + - -
17C LEU* 5.2 5.0 - - - +
72C MET* 4.3 21.2 - - + +
101C MET* 5.2 2.2 - - + +
102C LEU* 3.4 28.5 - - + -
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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