Contacts of the strand formed by residues 98 - 110 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A SER* 4.9 4.7 - - - +
46A TRP 3.4 11.4 - - - +
47A LYS* 4.0 18.1 - - - +
93A VAL* 3.4 0.4 - - - -
94A SER* 2.4 48.0 + - - +
96A ASP* 2.7 28.7 + - - -
97A GLY* 1.3 78.9 - - - +
99A VAL* 1.3 69.4 + - - +
100A GLN* 4.5 12.1 - - - +
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Residues in contact with VAL 99 (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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45A SER* 3.1 9.5 - - - -
46A TRP* 2.8 79.9 + - + +
48A ASP* 4.4 4.0 - - + -
51A LEU* 4.2 11.4 - - + -
70A ILE* 4.5 5.2 - - + -
91A ILE* 3.6 26.9 - - + -
92A SER 4.0 1.8 - - - +
93A VAL* 3.6 23.3 - - + +
97A GLY 4.0 8.1 - - - +
98A THR* 1.3 74.4 - - - +
100A GLN* 1.3 63.5 + - - +
101A TYR 3.9 0.8 + - - -
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Residues in contact with GLN 100 (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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44A LEU 4.0 1.5 - - - +
45A SER* 3.4 22.2 - - - -
90A ASP* 3.7 2.4 - - - +
91A ILE* 3.4 3.3 - - - -
92A SER* 2.8 53.4 + - - +
94A SER* 3.7 20.5 + - - +
98A THR* 4.5 7.4 - - + +
99A VAL* 1.3 74.6 - - - +
101A TYR* 1.3 58.6 + - - +
102A LEU* 4.2 0.6 + - - -
146A GLU* 5.8 0.3 - - - +
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Residues in contact with TYR 101 (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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42A LEU* 4.8 1.6 - - + -
43A SER* 3.7 2.9 - - - -
44A LEU* 2.8 67.8 + - + +
46A TRP* 3.5 21.8 - + + -
67A PRO* 5.1 2.0 - - + -
72A ILE* 3.9 21.8 - - + -
88A VAL* 4.0 23.3 - - + +
90A ASP 3.6 2.0 - - - -
91A ILE* 3.5 36.6 - - + +
99A VAL 3.9 0.2 - - - -
100A GLN* 1.3 72.9 + - - +
102A LEU* 1.3 63.8 + - - +
103A GLU* 2.7 48.6 + - + +
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Residues in contact with LEU 102 (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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41A PHE* 3.6 29.2 - - + -
42A LEU 3.5 16.4 - - - +
43A SER* 3.6 7.9 - - - +
88A VAL* 4.1 1.7 - - - +
89A VAL* 3.0 21.0 + - + +
90A ASP* 2.9 41.3 + - + +
100A GLN 5.7 0.2 - - - -
101A TYR* 1.3 78.4 - - - +
103A GLU* 1.3 59.2 + - - +
132C ARG* 3.4 46.2 - - - +
176C GLU* 3.2 23.6 - - - +
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Residues in contact with GLU 103 (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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41A PHE* 3.0 14.2 - - - -
42A LEU* 2.9 53.3 + - + +
84A ARG* 2.4 43.1 + - - -
86A ALA* 4.0 13.9 - - - +
87A ASP 3.5 16.6 - - - +
88A VAL* 4.4 0.8 - - - +
89A VAL* 3.9 3.6 - - - +
101A TYR* 2.7 41.8 + - + +
102A LEU* 1.3 75.5 - - - +
104A ARG* 1.3 65.1 + - - +
105A PHE* 4.1 1.4 - - - +
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Residues in contact with ARG 104 (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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24A ILE* 3.5 24.9 - - + +
39A ASN* 2.6 37.6 + - - +
40A ALA 3.1 18.4 - - - +
41A PHE* 4.0 11.4 - - + -
85A ASP 4.1 0.2 - - - +
86A ALA* 3.6 2.1 - - - -
87A ASP* 3.2 33.2 + - + +
89A VAL* 4.1 8.2 - - + +
103A GLU* 1.3 77.6 - - - +
105A PHE* 1.3 61.1 + - - +
76C ARG* 3.1 38.4 - - - +
77C PHE 2.9 21.0 + - - +
78C VAL* 3.2 26.2 + - - +
80C VAL* 5.0 1.4 + - - +
130C ILE* 5.0 1.2 - - - +
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Residues in contact with PHE 105 (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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21A ILE* 4.1 13.0 - - + -
38A VAL* 3.8 24.0 - - + -
39A ASN* 2.7 24.7 + - - -
40A ALA* 2.9 55.5 + - + -
41A PHE 3.9 10.3 - - - -
42A LEU* 4.0 18.2 - - + -
77A PHE* 3.4 38.8 - + - -
84A ARG* 3.3 26.7 - - + +
85A ASP 3.2 8.5 - - - +
86A ALA* 4.5 0.7 - - + -
103A GLU* 4.1 3.8 - - - +
104A ARG* 1.3 75.5 - - - +
106A SER* 1.3 60.0 + - - +
107A ALA* 4.1 12.6 - - + -
127A ILE* 5.6 1.1 - - + -
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Residues in contact with SER 106 (chain A).
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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27A TYR* 5.0 0.2 - - - -
38A VAL 3.4 7.9 - - - -
39A ASN* 3.8 16.6 - - - -
84A ARG* 4.6 0.2 - - - -
85A ASP* 3.1 40.8 + - - +
105A PHE* 1.3 75.8 - - - +
107A ALA* 1.3 62.1 + - - +
81C GLU 4.2 5.8 - - - -
82C ASN* 3.6 33.7 + - - +
83C ALA* 4.5 3.7 + - - +
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Residues in contact with ALA 107 (chain A).
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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27A TYR* 5.6 0.2 + - - -
37A LYS* 3.7 3.4 - - - +
38A VAL* 2.9 35.7 + - + +
77A PHE* 4.9 4.3 - - + -
80A VAL* 4.5 16.2 - - + -
84A ARG* 4.5 17.3 - - + +
105A PHE* 4.1 19.7 - - + -
106A SER* 1.3 76.1 - - - +
108A ARG* 1.3 67.0 + - - +
109A VAL* 4.0 1.3 - - + -
82C ASN* 5.9 2.2 - - - +
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Residues in contact with ARG 108 (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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28A SER 5.5 2.2 + - - -
30A ASP* 4.6 8.1 + - - +
33A ALA* 4.1 9.5 - - - +
35A THR* 2.5 35.4 + - - +
36A PHE 3.2 10.7 + - - +
37A LYS* 3.9 31.2 - - + +
80A VAL* 3.3 25.1 - - + +
81A GLU* 3.7 40.6 + - + +
82A ASN* 5.2 6.7 - - - +
107A ALA* 1.3 73.9 - - - +
109A VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 109 (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 THR* 3.2 8.9 - - - -
36A PHE* 2.9 55.6 + - + -
38A VAL* 4.1 19.5 - - + -
77A PHE* 5.0 2.2 - - + -
79A ASN* 3.1 28.0 - - - +
80A VAL* 4.5 7.4 - - + -
107A ALA* 4.8 4.0 - - + +
108A ARG* 1.3 76.9 - - - +
110A LEU* 1.3 63.1 + - - +
111A SER 3.9 0.8 + - - -
126A HIS 3.1 28.3 - - - +
127A ILE* 4.0 17.9 - - + -
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Residues in contact with LEU 110 (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 ALA 4.4 5.8 - - - +
34A GLU* 3.8 15.3 - - + +
35A THR* 3.7 16.2 - - + -
79A ASN* 2.7 45.5 + - + +
80A VAL* 4.4 4.9 - - - +
81A GLU* 3.8 11.0 - - + +
108A ARG 4.0 0.6 + - - -
109A VAL* 1.3 75.1 - - - +
111A SER* 1.3 60.1 + - - +
112A PRO* 4.4 2.2 - - + +
25D GLU* 4.1 19.6 - - + +
26D CYS 4.8 0.4 - - - +
27D TYR* 3.7 45.8 - - + -
155D PHE* 4.8 15.7 - - + -
157D THR* 6.1 1.8 - - + -
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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