Contacts of the helix formed by residues 84 - 102 (chain A) in PDB entry 5LSW
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 ALA 84 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A THR* 1.3 74.8 - - - +
85A HIS* 1.3 57.2 + - - +
87A SER* 3.4 0.7 + - - -
88A ASN* 2.9 30.7 + - - +
130A ARG* 6.4 1.1 - - - -
131A PRO* 3.7 22.6 - - + +
791B GLY 4.3 2.0 - - - -
792B GLY* 4.1 17.0 - - - -
793B ILE* 3.7 18.0 - - + +
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Residues in contact with HIS 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU* 2.6 37.5 + - - -
83A THR* 3.2 8.3 + - - +
84A ALA* 1.3 76.0 - - - +
86A GLN* 1.3 71.0 + - - +
88A ASN* 3.4 4.2 + - - +
89A ARG* 3.1 30.0 + - - +
790B GLU 4.5 6.3 - - - +
791B GLY* 3.3 38.8 + - - +
792B GLY* 4.7 0.8 - - - -
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Residues in contact with GLN 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASN 5.4 1.8 + - - -
73A ILE* 4.3 16.5 - - + +
76A SER* 3.2 22.7 + - - -
81A THR 3.9 1.6 - - - +
82A LEU* 3.4 23.2 - - + -
83A THR* 2.9 43.2 + - - +
85A HIS* 1.3 81.6 + - - +
87A SER* 1.3 64.1 + - - +
89A ARG* 3.3 7.5 + - - +
90A VAL* 3.0 25.9 + - - +
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Residues in contact with SER 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.8 11.1 - - - +
83A THR 3.0 17.7 + - - -
84A ALA 3.8 3.4 - - - -
86A GLN* 1.3 76.2 - - - +
88A ASN* 1.3 63.8 + - - +
90A VAL* 3.2 10.4 - - - +
91A CYS* 2.9 28.6 + - - -
131A PRO* 2.7 35.7 + - - -
134A TYR* 3.8 14.1 - - - -
135A LEU* 3.8 8.3 - - - +
793B ILE* 3.9 2.0 - - - +
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Residues in contact with ASN 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU* 5.8 1.8 + - - -
40A LEU* 6.0 2.3 - - - +
84A ALA 2.9 18.6 + - - +
85A HIS* 3.7 6.2 + - - +
87A SER* 1.3 77.7 - - - +
89A ARG* 1.3 63.4 + - - +
91A CYS* 3.3 1.7 + - - +
92A ASN* 3.1 38.2 + - - +
134A TYR* 4.2 11.1 + - - -
791B GLY* 3.7 15.8 + - - +
792B GLY 3.7 18.7 + - - +
793B ILE* 4.3 4.7 - - + +
797B MET* 3.3 25.6 - - - +
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Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PRO* 4.6 10.5 + - - +
35A ARG* 4.0 18.8 - - - +
36A GLU* 3.3 53.6 + - + +
39A LEU* 3.9 15.1 - - + +
69A GLU* 2.7 42.5 + - - +
72A ASN* 5.7 1.6 - - - +
85A HIS* 3.1 22.5 + - + +
86A GLN* 3.7 6.5 - - - +
88A ASN* 1.3 81.5 - - - +
90A VAL* 1.3 63.1 + - - +
92A ASN* 3.1 20.4 + - - +
93A ALA 3.2 8.1 + - - -
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Residues in contact with VAL 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU* 4.2 10.3 - - - +
70A ILE* 3.8 37.7 - - + +
73A ILE* 3.6 30.7 - - + -
86A GLN 3.0 19.3 + - - +
87A SER* 3.2 17.3 - - - +
89A ARG* 1.3 78.4 - - - +
91A CYS* 1.3 56.5 + - - +
93A ALA* 3.0 8.3 + - - +
94A LEU* 2.8 31.7 + - + +
122A PHE* 4.4 5.8 - - + -
135A LEU* 3.8 9.4 - - + -
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Residues in contact with CYS 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER* 2.9 25.2 + - - +
88A ASN 3.8 1.6 - - - +
90A VAL* 1.3 75.2 - - - +
92A ASN* 1.3 61.5 + - - +
94A LEU* 3.6 8.5 - - - +
95A ALA* 2.8 27.9 + - - +
134A TYR* 3.5 33.2 - - + +
135A LEU* 3.7 28.7 - - - -
138A THR* 3.5 30.5 - - + +
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Residues in contact with ASN 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLU* 5.0 2.2 + - - +
39A LEU* 4.0 21.8 - - + +
40A LEU* 3.7 32.1 - - - +
43A SER* 3.7 19.0 + - - +
88A ASN* 3.1 36.4 + - - +
89A ARG* 3.1 11.8 + - - +
91A CYS* 1.3 78.4 - - - +
93A ALA* 1.3 60.5 + - - +
95A ALA* 3.3 9.5 + - - +
96A LEU* 3.3 24.1 + - - +
134A TYR* 5.2 3.6 + - - -
797B MET* 5.7 0.5 - - - +
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Residues in contact with ALA 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.8 21.0 - - + +
66A LEU* 4.0 19.8 - - + +
69A GLU* 4.1 23.6 - - + -
70A ILE* 5.0 4.7 - - + -
89A ARG 3.2 6.4 + - - +
90A VAL* 3.0 9.9 + - - +
92A ASN* 1.3 78.4 - - - +
94A LEU* 1.3 63.6 + - - +
96A LEU* 3.2 6.1 + - - +
97A LEU* 3.0 25.7 + - - +
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 3.6 28.9 - - + -
90A VAL* 2.8 24.4 + - + +
91A CYS* 3.6 8.5 - - - +
92A ASN 3.3 0.2 - - - -
93A ALA* 1.3 70.2 - - - +
95A ALA* 1.3 61.1 + - - +
97A LEU* 3.1 7.8 + - + +
98A GLN* 2.8 29.3 + - - +
119A LEU* 3.7 27.6 - - + -
122A PHE* 4.4 4.9 - - + -
135A LEU* 3.9 21.1 - - + -
138A THR* 3.7 23.6 - - + -
139A SER* 3.6 22.4 - - - +
142A VAL* 3.6 9.4 - - + +
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A SER* 4.3 15.5 - - - +
46A ARG* 3.1 37.1 - - - +
91A CYS 2.8 17.5 + - - +
92A ASN* 3.5 7.6 - - - +
93A ALA 3.3 0.2 - - - -
94A LEU* 1.3 76.2 - - - +
96A LEU* 1.3 61.5 + - - +
98A GLN* 3.3 15.4 + - - +
99A CYS 3.4 3.6 + - - -
138A THR* 4.7 4.0 - - + +
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Residues in contact with LEU 96 (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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29A LEU* 4.5 4.3 - - + -
39A LEU* 4.0 24.2 - - + +
42A LEU* 3.9 51.8 - - + +
43A SER* 4.0 8.1 - - - +
46A ARG* 5.1 3.4 - - + -
52A LEU* 4.0 19.7 - - + -
56A LEU* 3.9 16.6 - - + +
66A LEU* 4.1 14.6 - - + -
92A ASN 3.3 9.4 + - - +
93A ALA 3.2 7.9 + - - +
94A LEU 3.2 0.4 - - - -
95A ALA* 1.3 76.1 - - - +
97A LEU* 1.3 64.3 + - - +
99A CYS* 3.3 8.5 + - - -
100A VAL* 3.2 25.7 + - - +
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Residues in contact with LEU 97 (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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57A TRP* 6.1 0.4 - - + -
63A ILE* 4.7 15.0 - - + -
66A LEU* 3.8 29.4 - - + -
67A LEU* 4.2 8.1 - - + -
70A ILE* 3.4 32.8 - - + -
93A ALA 3.0 16.3 + - - +
94A LEU* 3.1 13.7 + - + +
96A LEU* 1.3 77.0 - - - +
98A GLN* 1.3 58.1 + - - +
100A VAL* 3.2 7.7 + - + +
101A ALA* 2.9 29.1 + - - +
110A PHE* 3.7 20.1 - - + -
115A ILE* 4.0 21.3 - - + -
119A LEU* 4.8 3.4 - - + -
142A VAL* 4.5 6.5 - - + -
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Residues in contact with GLN 98 (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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46A ARG* 3.3 25.0 - - - +
94A LEU 2.8 16.9 + - - +
95A ALA* 3.5 13.0 - - - +
96A LEU 3.2 0.2 - - - -
97A LEU* 1.3 73.3 - - - +
99A CYS* 1.3 61.3 + - - +
101A ALA* 3.2 10.4 + - - +
102A SER* 3.1 17.6 + - - +
138A THR* 4.7 3.6 - - - +
141A GLY* 3.6 22.1 - - - -
142A VAL* 3.8 21.8 + - + +
145A ALA* 3.7 18.3 - - + +
804B ASN* 3.3 32.6 + - - +
808B ILE* 3.8 8.5 - - - +
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Residues in contact with CYS 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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46A ARG* 3.8 30.2 - - + +
52A LEU* 4.3 23.8 - - - -
53A ALA* 3.3 34.8 - - - +
56A LEU* 4.4 2.7 - - - -
95A ALA 3.4 2.2 + - - -
96A LEU* 3.3 15.0 + - - +
97A LEU 3.3 0.4 - - - -
98A GLN* 1.3 77.4 - - - +
100A VAL* 1.3 67.2 + - - +
102A SER* 3.5 8.7 + - - +
103A HIS* 3.3 16.3 + - - +
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Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ALA* 3.6 28.5 - - + +
56A LEU* 4.1 15.7 - - + -
57A TRP* 3.5 28.9 - - + -
63A ILE* 4.6 10.5 - - + -
66A LEU* 5.8 0.2 - - + -
96A LEU 3.2 16.3 + - - +
97A LEU* 3.2 12.5 + - + +
99A CYS* 1.3 78.4 - - - +
101A ALA* 1.3 61.4 + - - +
102A SER 3.3 0.7 + - - -
103A HIS 3.6 3.3 + - - -
106A THR* 2.8 27.4 + - - +
107A ARG* 3.8 8.0 - - - -
110A PHE* 3.6 17.5 - - + -
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU 2.9 16.3 + - - +
98A GLN* 3.2 10.5 + - - +
100A VAL* 1.3 77.1 - - - +
102A SER* 1.3 56.4 + - - +
107A ARG* 3.4 20.4 + - - +
110A PHE* 3.5 33.4 - - + -
142A VAL* 4.4 8.1 - - + +
145A ALA 5.4 0.2 - - - -
146A LEU* 3.4 31.5 - - + +
149A THR* 4.6 0.2 - - - +
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Residues in contact with SER 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLN* 3.1 16.6 + - - +
99A CYS* 3.5 10.6 + - - +
101A ALA* 1.3 76.4 - - - +
103A HIS* 1.3 61.1 + - - +
104A PRO* 3.7 2.9 - - - +
107A ARG* 3.0 19.8 + - - -
145A ALA* 4.4 22.7 - - - +
149A THR* 4.5 9.7 - - - +
193C ASP* 4.4 1.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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