Contacts of the strand formed by residues 98 - 110 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D SER* 5.3 4.5 - - - -
46D TRP 3.8 6.3 - - - +
47D LYS* 4.3 12.0 + - - +
93D VAL* 3.2 1.0 - - - -
94D SER* 2.4 56.2 + - - +
96D ASP* 2.8 20.8 + - - -
97D GLY* 1.3 78.5 - - - +
99D VAL* 1.3 64.0 + - - +
100D GLN* 3.9 24.0 + - - +
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Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D SER* 3.2 8.8 - - - -
46D TRP* 2.8 85.6 + - + +
48D ASP* 4.3 7.4 - - + +
51D LEU* 4.3 8.7 - - + -
70D ILE* 4.7 6.7 - - + -
91D ILE* 4.1 15.9 - - + -
92D SER 4.0 1.6 - - - -
93D VAL* 3.6 29.4 - - + +
97D GLY 4.0 7.9 - - - +
98D THR* 1.3 75.8 - - - +
100D GLN* 1.3 64.6 + - - +
101D TYR 3.9 0.4 + - - -
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Residues in contact with GLN 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU 3.9 2.0 - - - +
45D SER* 3.5 18.2 - - - -
90D ASP 3.8 1.0 - - - +
91D ILE* 3.4 5.5 - - - +
92D SER* 2.9 54.6 + - - +
94D SER* 4.1 15.5 + - - +
98D THR* 4.0 17.7 - - + +
99D VAL* 1.3 74.2 - - - +
101D TYR* 1.3 60.3 + - - +
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Residues in contact with TYR 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D LEU* 4.8 2.5 - - + -
43D SER* 3.8 2.1 - - - -
44D LEU* 2.9 70.6 + - + +
46D TRP* 3.6 23.3 - + + -
67D PRO* 5.5 1.3 - - + -
72D ILE* 4.4 20.0 - - + -
88D VAL* 3.7 30.5 - - + +
90D ASP 3.7 1.3 - - - -
91D ILE* 3.6 28.5 - - + +
99D VAL* 3.9 1.7 - - + -
100D GLN* 1.3 74.1 - - - +
102D LEU* 1.3 62.5 + - - +
103D GLU* 2.2 54.3 + - + +
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Residues in contact with LEU 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ARG* 3.7 39.0 - - - +
176A GLU* 3.3 24.2 - - - +
41D PHE* 3.4 33.9 - - + -
42D LEU 3.3 17.9 - - - +
43D SER* 4.0 5.8 - - - +
88D VAL* 3.9 1.2 - - - +
89D VAL* 2.8 35.1 + - + +
90D ASP* 2.9 31.9 + - + +
100D GLN 5.8 0.2 - - - -
101D TYR* 1.3 77.8 - - - +
103D GLU* 1.3 60.0 + - - +
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Residues in contact with GLU 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D PHE* 3.1 13.2 - - - -
42D LEU* 3.0 49.4 + - + +
84D ARG* 2.2 46.8 + - - -
86D ALA* 3.6 13.3 - - - +
87D ASP 3.2 15.0 - - - +
88D VAL* 3.9 5.1 - - - +
89D VAL* 3.7 2.7 - - - +
101D TYR* 2.2 45.4 + - + +
102D LEU* 1.3 74.8 - - - +
104D ARG* 1.3 65.1 + - - +
105D PHE 4.8 0.2 - - - +
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Residues in contact with ARG 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ARG* 3.5 34.1 - - - +
77A PHE 2.9 22.4 + - - +
78A VAL* 3.3 23.0 + - - +
80A VAL* 4.8 2.0 + - - +
130A ILE* 5.3 1.2 - - - +
24D ILE* 3.6 29.3 - - + +
39D ASN* 2.6 36.3 + - - +
40D ALA 3.2 16.2 - - - +
41D PHE* 4.1 12.8 - - + -
86D ALA* 3.4 1.6 - - - -
87D ASP* 2.8 41.6 + - + +
89D VAL* 4.1 8.9 - - + +
103D GLU* 1.3 75.4 - - - +
105D PHE* 1.3 61.2 + - - +
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Residues in contact with PHE 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ILE* 4.9 9.0 - - + -
38D VAL* 4.0 21.3 - - + -
39D ASN* 2.8 18.4 + - - -
40D ALA* 2.9 57.2 + - + -
41D PHE 3.9 10.8 - - - -
42D LEU* 3.9 19.1 - - + -
77D PHE* 3.5 39.0 - + - -
84D ARG* 3.6 28.9 - - + +
85D ASP 3.4 7.4 - - - +
86D ALA* 3.7 7.0 - - + -
103D GLU* 4.2 0.9 - - - +
104D ARG* 1.3 74.3 - - - +
106D SER* 1.3 63.0 + - - +
107D ALA* 4.0 15.7 - - + -
127D ILE* 5.8 0.7 - - + -
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Residues in contact with SER 106 (chain D).
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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81A GLU 3.9 17.3 - - - -
82A ASN* 4.3 20.2 + - - +
83A ALA* 4.7 4.3 + - - +
27D TYR* 4.9 2.0 - - - -
38D VAL 3.4 8.3 - - - -
39D ASN* 3.5 14.1 - - - -
84D ARG* 4.2 0.2 - - - -
85D ASP* 3.0 36.5 + - - +
105D PHE* 1.3 74.4 - - - +
107D ALA* 1.3 60.0 + - - +
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Residues in contact with ALA 107 (chain D).
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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27D TYR* 5.5 0.3 + - - -
37D LYS* 3.7 3.5 - - - +
38D VAL* 2.9 35.9 + - + +
77D PHE* 5.3 1.8 - - + -
80D VAL* 4.1 21.3 - - + -
84D ARG* 3.6 26.0 - - + +
105D PHE* 4.0 14.3 - - + -
106D SER* 1.3 75.6 - - - +
108D ARG* 1.3 61.3 + - - +
109D VAL* 5.3 0.9 - - + -
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Residues in contact with ARG 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D SER 5.7 1.4 + - - -
30D ASP* 5.2 3.2 + - - +
33D ALA* 4.6 5.7 - - - +
35D THR* 2.4 38.1 + - - +
36D PHE 3.4 9.8 + - - +
37D LYS* 3.7 33.6 - - + +
80D VAL* 3.1 26.4 - - - +
81D GLU* 3.4 45.2 + - + +
82D ASN* 4.8 10.1 - - + +
107D ALA* 1.3 74.2 - - - +
109D VAL* 1.3 61.3 + - - +
37E LYS* 5.8 2.0 - - - +
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Residues in contact with VAL 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D THR* 3.4 6.4 - - - -
36D PHE* 2.9 53.5 + - + +
38D VAL* 3.8 18.4 - - + -
77D PHE* 5.4 1.6 - - + -
79D ASN* 3.3 19.3 - - - +
80D VAL* 4.5 8.3 - - + -
81D GLU* 5.5 0.4 - - - -
107D ALA* 5.0 1.6 - - + -
108D ARG* 1.3 76.6 - - - +
110D LEU* 1.3 62.7 + - - +
111D SER 3.9 0.9 + - - -
126D HIS 3.2 27.4 - - - +
127D ILE* 3.7 32.5 - - + -
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Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D ALA 4.8 3.6 - - - +
34D GLU* 3.7 15.5 - - + +
35D THR* 3.8 15.5 - - + -
79D ASN* 2.6 50.1 + - + +
80D VAL* 4.6 3.6 - - - +
81D GLU* 3.6 10.8 - - + +
108D ARG 4.0 0.8 + - - -
109D VAL* 1.3 70.9 - - - +
111D SER* 1.3 63.1 + - - +
112D PRO* 4.4 3.9 - - + +
25E GLU* 3.9 15.9 - - + +
26E CYS 4.7 1.1 - - - +
27E TYR* 3.6 46.4 - - + -
155E PHE* 5.5 15.3 - - + -
157E THR* 5.9 4.0 - - + -
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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