Contacts of the strand formed by residues 98 - 110 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C SER* 5.3 4.0 - - - -
46C TRP 3.8 7.8 - - - +
47C LYS* 4.4 14.0 - - - +
92C SER 3.6 1.4 - - - +
93C VAL* 3.2 1.1 - - - -
94C SER* 2.5 48.5 + - - +
96C ASP* 3.0 23.1 + - - -
97C GLY* 1.3 77.5 - - - +
99C VAL* 1.3 70.1 + - - +
100C GLN* 4.7 12.8 - - + +
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Residues in contact with VAL 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C SER* 3.1 11.8 - - - -
46C TRP* 2.9 80.8 + - + +
48C ASP* 4.4 1.3 - - + -
51C LEU* 3.6 31.2 - - + -
70C ILE* 4.9 3.6 - - + -
91C ILE* 3.9 25.6 - - + -
92C SER 3.8 2.2 - - - -
93C VAL* 3.7 10.1 - - + +
97C GLY 4.2 5.2 - - - +
98C THR* 1.3 75.4 - - - +
100C GLN* 1.3 64.5 + - - +
101C TYR 4.0 0.2 - - - -
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Residues in contact with GLN 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LEU 4.0 1.3 - - - +
45C SER* 3.8 16.1 - - - -
90C ASP 3.6 1.7 - - - +
91C ILE* 3.2 6.4 - - - +
92C SER* 2.9 56.1 + - - +
94C SER* 4.6 11.8 + - - +
98C THR* 4.7 10.0 - - + +
99C VAL* 1.3 75.1 - - - +
101C TYR* 1.3 60.6 + - - +
102C LEU* 5.7 0.2 - - - -
146C GLU* 5.6 1.4 - - - +
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Residues in contact with TYR 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU 4.7 0.9 - - - -
43C SER* 3.7 2.8 - - - -
44C LEU* 2.8 66.3 + - + +
46C TRP* 3.6 19.3 - + + -
67C PRO* 5.7 1.1 - - + -
72C ILE* 3.6 32.2 - - + +
84C ARG* 5.5 0.6 + - - -
88C VAL* 3.5 26.9 - - + +
90C ASP 3.6 3.4 - - - -
91C ILE* 3.6 29.6 - - + +
99C VAL* 4.0 0.6 - - + -
100C GLN* 1.3 73.9 + - - +
102C LEU* 1.3 64.5 + - - +
103C GLU* 2.7 44.1 + - + -
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Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ARG* 3.5 41.1 - - - +
176B GLU* 3.4 23.1 - - - +
41C PHE* 3.6 33.7 - - + -
42C LEU 3.3 15.7 - - - +
43C SER* 3.5 7.9 - - - +
88C VAL* 3.8 1.7 - - - +
89C VAL* 2.7 41.9 + - + +
90C ASP* 2.9 26.1 + - + +
100C GLN 5.7 0.2 - - - -
101C TYR* 1.3 79.1 - - - +
103C GLU* 1.3 52.9 + - - +
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Residues in contact with GLU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C PHE* 3.3 13.0 - - - -
42C LEU* 2.9 50.3 + - + +
44C LEU* 6.1 0.2 - - - -
84C ARG* 2.2 45.8 + - - -
86C ALA* 3.8 13.9 - - - +
87C ASP 3.2 15.0 - - - +
88C VAL* 3.9 8.1 - - - +
89C VAL* 3.6 3.4 - - - +
101C TYR* 2.7 34.6 + - + -
102C LEU* 1.3 74.8 - - - +
104C ARG* 1.3 64.2 + - - +
105C PHE* 4.1 0.7 - - - +
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Residues in contact with ARG 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ARG* 2.8 49.5 - - - +
77B PHE 2.5 24.4 + - - -
78B VAL* 2.7 31.1 + - - +
80B VAL* 6.0 0.2 - - - +
130B ILE* 4.3 1.0 - - - +
24C ILE* 3.3 33.1 - - + +
39C ASN* 3.1 29.5 + - - +
40C ALA 3.1 15.3 - - - +
41C PHE* 4.1 9.6 - - + -
85C ASP 4.2 0.2 - - - +
86C ALA* 3.5 0.6 - - - -
87C ASP* 2.8 40.5 + - + +
89C VAL* 4.0 7.5 - - + +
103C GLU* 1.3 74.1 - - - +
105C PHE* 1.3 60.7 + - - +
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Residues in contact with PHE 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ILE* 4.6 10.5 - - + -
38C VAL* 3.8 23.3 - - + -
39C ASN* 3.0 6.4 - - - +
40C ALA* 2.9 64.9 + - + -
41C PHE 4.0 9.0 - - - -
42C LEU* 4.0 22.4 - - + -
77C PHE* 3.3 42.4 - + - -
84C ARG* 3.5 26.5 - - + +
85C ASP 3.2 11.7 - - - +
86C ALA* 4.0 1.8 - - + -
103C GLU* 4.1 0.4 - - - +
104C ARG* 1.3 76.5 - - - +
106C SER* 1.3 65.1 + - - +
107C ALA* 4.1 11.4 - - + -
127C ILE* 5.8 0.4 - - + -
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Residues in contact with SER 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B GLU 3.7 22.9 - - - -
82B ASN* 3.7 27.5 + - - +
83B ALA* 4.1 5.0 + - - +
27C TYR* 4.5 1.1 - - - -
38C VAL 3.3 7.9 - - - -
39C ASN* 3.8 7.4 - - - -
84C ARG* 4.0 0.3 - - - -
85C ASP* 2.8 41.7 + - - +
105C PHE* 1.3 76.5 - - - +
107C ALA* 1.3 60.4 + - - +
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Residues in contact with ALA 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ASN* 6.3 0.2 - - - -
27C TYR* 5.2 1.4 + - - -
37C LYS* 3.6 3.8 - - - +
38C VAL* 2.9 36.0 + - + +
77C PHE* 4.8 3.1 - - + -
80C VAL* 4.2 19.3 - - + -
83C ALA 5.7 0.4 - - - -
84C ARG* 3.7 25.8 - - + +
105C PHE* 4.1 13.3 - - + -
106C SER* 1.3 75.4 - - - +
108C ARG* 1.3 62.5 + - - +
109C VAL* 4.0 0.4 - - + -
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Residues in contact with ARG 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LYS* 5.6 2.8 - - - +
28C SER 5.1 3.2 + - - -
30C ASP* 4.4 9.9 + - - +
33C ALA* 4.3 9.2 - - - +
35C THR* 2.1 39.8 + - - +
36C PHE 3.3 10.0 + - - +
37C LYS* 3.7 31.8 - - + +
80C VAL* 3.0 22.2 - - - +
81C GLU* 3.3 42.7 + - + +
82C ASN* 5.1 5.1 + - - +
107C ALA* 1.3 74.3 - - - +
109C VAL* 1.3 60.0 + - - +
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Residues in contact with VAL 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C THR* 3.2 5.7 - - - -
36C PHE* 2.9 50.9 + - + +
38C VAL* 3.8 15.5 - - + -
77C PHE* 5.1 1.1 - - + -
79C ASN* 3.1 29.6 - - - +
80C VAL* 4.6 7.4 - - + -
81C GLU* 5.2 0.2 - - - -
107C ALA* 5.0 1.8 - - + -
108C ARG* 1.3 76.3 - - - +
110C LEU* 1.3 60.9 + - - +
111C SER 3.8 0.7 + - - -
126C HIS 3.1 27.6 - - - +
127C ILE* 3.7 31.4 - - + -
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Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLU* 4.1 17.8 - - + +
26A CYS 4.6 0.7 - - - +
27A TYR* 3.4 38.4 - - + -
155A PHE* 4.3 24.0 - - + -
157A THR* 5.3 2.2 - - + -
33C ALA 4.1 6.5 - - - +
34C GLU* 3.4 16.8 - - + +
35C THR* 3.5 7.0 - - + -
79C ASN* 2.9 39.6 + - + +
80C VAL 4.5 2.2 - - - +
81C GLU* 3.3 31.9 - - + +
108C ARG 4.0 0.8 + - - -
109C VAL* 1.3 76.3 - - - +
111C SER* 1.3 57.7 + - - +
112C PRO* 4.3 2.4 - - - +
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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