Contacts of the strand formed by residues 98 - 110 (chain E) in PDB entry 4LML
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 THR 98 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45E SER* 5.5 2.5 - - - -
46E TRP 4.0 11.0 - - - +
47E LYS* 4.2 20.2 - - - +
92E SER 3.5 3.3 - - - +
94E SER* 2.8 46.5 + - - +
96E ASP* 3.2 19.4 + - - -
97E GLY* 1.3 76.9 - - - +
99E VAL* 1.3 68.6 + - - +
100E GLN* 3.9 14.8 + - + +
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Residues in contact with VAL 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E SER* 3.3 8.1 - - - -
46E TRP* 2.9 78.2 + - + +
48E ASP* 4.2 2.9 - - + -
51E LEU* 3.5 31.0 - - + -
70E ILE* 4.7 4.3 - - + -
91E ILE* 4.0 25.1 - - + -
92E SER 3.8 1.8 - - - +
93E VAL* 4.1 9.4 - - + +
97E GLY 4.1 5.2 - - - +
98E THR* 1.3 75.5 - - - +
100E GLN* 1.3 63.9 + - - +
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Residues in contact with GLN 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E LEU 4.2 2.1 - - - +
45E SER* 3.3 24.9 - - - -
90E ASP* 3.7 2.1 - - - +
91E ILE* 3.3 5.7 - - - +
92E SER* 2.9 50.8 + - - +
94E SER* 5.0 5.1 + - - +
98E THR* 4.7 15.2 - - + +
99E VAL* 1.3 74.7 - - - +
101E TYR* 1.3 60.3 + - - +
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Residues in contact with TYR 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E LEU 4.7 0.9 - - - -
43E SER* 3.8 2.4 - - - -
44E LEU* 2.9 69.4 + - + +
46E TRP* 3.7 18.2 - - + -
67E PRO* 5.3 1.6 - - + -
72E ILE* 4.1 23.6 - - + -
88E VAL* 3.8 30.9 - - + +
90E ASP 3.6 2.2 - - - -
91E ILE* 3.7 26.2 - - + +
99E VAL* 4.1 1.7 - - + -
100E GLN* 1.3 73.2 + - - +
102E LEU* 1.3 62.7 + - - +
103E GLU* 2.6 51.2 + - + +
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Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ARG* 3.9 27.8 - - - +
176D GLU* 4.3 14.4 - - - +
41E PHE* 3.4 45.5 - - + -
42E LEU 3.2 19.3 - - - +
43E SER* 4.4 3.1 - - - +
88E VAL* 4.0 2.1 - - - +
89E VAL* 2.9 41.8 + - + -
90E ASP* 2.9 25.2 + - + +
100E GLN 4.2 0.2 - - - -
101E TYR* 1.3 79.0 - - - +
103E GLU* 1.3 61.0 + - - +
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Residues in contact with GLU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E PHE* 3.1 13.0 - - - -
42E LEU* 2.9 52.4 + - + +
84E ARG* 2.2 45.6 + - - -
86E ALA* 3.8 12.7 - - - +
87E ASP 3.4 13.5 - - - +
88E VAL* 4.1 3.0 - - - +
89E VAL* 3.8 2.5 - - - +
101E TYR* 2.6 42.1 + - + +
102E LEU* 1.3 77.2 - - - +
104E ARG* 1.3 65.8 + - - +
105E PHE* 3.7 3.9 - - - +
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Residues in contact with ARG 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D ARG* 3.2 39.6 - - - +
77D PHE 2.8 22.6 + - - +
78D VAL* 3.2 24.4 + - - +
80D VAL* 4.9 0.4 + - - +
130D ILE* 4.9 0.6 - - - +
24E ILE* 3.4 32.3 - - + +
39E ASN* 2.7 33.1 + - - +
40E ALA 3.3 16.4 - - - +
41E PHE* 4.0 10.5 - - + -
85E ASP 4.1 0.2 - - - +
86E ALA* 3.4 0.7 - - - -
87E ASP* 2.9 39.3 + - + +
89E VAL* 4.2 8.0 - - + +
103E GLU* 1.3 76.3 - - - +
105E PHE* 1.3 59.2 - - - +
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Residues in contact with PHE 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E ILE* 4.4 9.9 - - + -
38E VAL* 3.8 23.8 - - + -
39E ASN* 2.9 5.1 + - - -
40E ALA* 2.9 65.9 + - + -
41E PHE 4.1 9.0 - - - -
42E LEU* 4.1 15.7 - - + -
77E PHE* 3.4 37.5 - + - -
84E ARG* 3.4 27.8 - - + +
85E ASP 3.0 12.3 - - - +
86E ALA* 3.9 3.4 - - + -
103E GLU* 3.7 7.6 - - - +
104E ARG* 1.3 75.0 - - - +
106E SER* 1.3 63.9 + - - +
107E ALA* 4.1 13.5 - - + -
127E ILE* 5.4 0.9 - - + -
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Residues in contact with SER 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D GLU 3.8 16.2 - - - -
82D ASN* 4.1 22.4 + - - -
83D ALA* 4.2 5.9 + - - +
27E TYR* 5.0 1.3 - - - -
38E VAL 3.3 9.9 - - - -
39E ASN* 3.5 15.9 - - - -
85E ASP* 2.8 42.8 + - - +
105E PHE* 1.3 73.0 - - - +
107E ALA* 1.3 60.3 + - - +
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Residues in contact with ALA 107 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E LYS* 3.8 3.6 - - - +
38E VAL* 2.9 36.4 + - + +
77E PHE* 5.3 1.1 - - + -
80E VAL* 4.0 24.9 - - + -
83E ALA 5.9 0.2 - - - -
84E ARG* 4.1 22.9 - - + +
105E PHE* 4.1 14.7 - - + -
106E SER* 1.3 75.3 - - - +
108E ARG* 1.3 60.0 + - - +
109E VAL* 4.0 0.9 - - + -
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Residues in contact with ARG 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B LYS* 6.2 0.2 - - - +
28E SER 5.6 2.4 + - - -
30E ASP* 4.8 6.5 + - - +
33E ALA* 4.5 8.1 - - - +
35E THR* 2.6 32.5 + - - +
36E PHE 3.5 4.5 - - - +
37E LYS* 3.5 41.3 - - + +
80E VAL* 3.1 22.3 - - + +
81E GLU* 3.4 46.4 + - + +
82E ASN* 5.1 8.3 - - - +
107E ALA* 1.3 72.6 - - - +
109E VAL* 1.3 61.0 + - - +
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Residues in contact with VAL 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E THR* 3.1 7.1 - - - -
36E PHE* 2.8 61.4 + - + +
38E VAL* 4.0 16.6 - - + -
77E PHE* 5.6 1.1 - - + -
79E ASN* 3.5 19.5 - - - +
80E VAL* 4.5 7.2 - - + -
81E GLU* 5.3 0.2 - - - -
107E ALA* 4.7 1.1 - - + +
108E ARG* 1.3 73.5 - - - +
110E LEU* 1.3 64.4 + - - +
111E SER 4.0 0.2 - - - -
126E HIS 3.2 27.6 - - - +
127E ILE* 3.7 29.6 - - + -
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Residues in contact with LEU 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B GLU* 4.6 19.5 - - + +
26B CYS 4.7 1.3 - - - +
27B TYR* 3.4 44.0 - - + -
155B PHE* 4.4 24.2 - - + -
157B THR* 5.8 1.6 - - + -
33E ALA 4.4 6.5 - - - +
34E GLU* 3.8 11.7 - - + +
35E THR* 3.6 7.9 - - + -
79E ASN* 3.1 37.3 + - + +
80E VAL 4.5 1.1 - - - +
81E GLU* 3.4 26.9 - - + +
108E ARG 3.9 0.8 + - - -
109E VAL* 1.3 74.1 - - - +
111E SER* 1.3 62.1 - - - +
112E PRO* 4.5 1.7 - - - +
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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