Contacts of the helix formed by residues 130 - 148 (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 ARG 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A LYS 3.9 0.4 + - - -
129A THR* 1.3 72.7 - - - +
131A PRO* 1.3 70.9 - - + +
133A GLU* 4.1 5.6 - - - +
134A TYR* 3.0 27.5 + - - +
301A SO4 3.3 48.9 + - - +
793B ILE* 3.0 37.5 + - + +
794B ASP 3.4 22.0 + - - -
795B SER* 3.4 21.7 + - - +
798B MET* 3.5 31.0 - - + +
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Residues in contact with PRO 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.7 26.9 - - + +
83A THR* 3.7 12.8 - - - +
84A ALA* 3.7 26.7 - - + +
87A SER* 2.7 25.0 + - - +
129A THR* 3.5 14.8 - - - +
130A ARG* 1.3 94.9 - - + +
132A PHE* 1.3 59.2 + - + +
135A LEU* 3.3 10.9 + - - +
793B ILE* 3.9 11.2 - - + -
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Residues in contact with PHE 132 (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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76A SER 4.0 2.9 - - - -
77A ILE* 3.9 17.0 - - + -
80A PRO* 3.5 40.4 - - + -
82A LEU* 3.6 39.9 - - + -
125A THR* 3.7 39.4 + - + -
127A SER* 3.4 29.4 - - - +
129A THR* 3.2 23.5 + - + +
131A PRO* 1.3 76.7 - - - +
133A GLU* 1.3 62.0 + - - +
135A LEU* 3.3 6.9 + - + +
136A ARG* 2.8 36.0 + - - +
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Residues in contact with GLU 133 (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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128A LYS* 4.8 9.3 - - + +
129A THR 2.9 18.9 + - - +
130A ARG* 4.1 4.0 - - - +
132A PHE* 1.3 76.0 - - - +
134A TYR* 1.3 57.2 + - - +
136A ARG* 2.8 38.8 + - - +
137A LEU* 2.8 45.5 + - + +
175A SER* 2.4 37.4 + - - -
177A LEU* 5.4 0.2 - - - +
178A SER* 3.1 12.3 + - - -
798B MET* 3.7 22.0 - - + -
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Residues in contact with TYR 134 (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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87A SER* 3.8 2.9 - - - -
88A ASN* 4.2 14.4 + - - -
91A CYS* 3.5 38.0 - - + +
92A ASN* 5.2 3.3 + - - -
130A ARG 3.0 18.4 + - - +
131A PRO 4.1 0.9 - - - +
133A GLU* 1.3 76.6 - - - +
135A LEU* 1.3 54.8 + - - +
138A THR* 2.7 39.3 + - - -
793B ILE* 3.6 32.1 - - + -
797B MET* 3.4 48.2 + - + +
798B MET* 3.7 23.0 - - - +
801B LEU* 3.7 27.6 - - + +
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Residues in contact with LEU 135 (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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73A ILE* 4.1 0.4 - - + -
77A ILE* 4.0 9.6 - - + -
82A LEU* 3.8 20.2 - - + -
87A SER* 3.8 4.9 + - - +
90A VAL* 3.8 28.0 - - + -
91A CYS* 3.7 7.0 - - - -
94A LEU* 3.9 10.1 - - + -
122A PHE* 3.5 56.5 - - + +
125A THR* 5.5 0.4 - - - +
131A PRO 3.3 16.2 + - - +
132A PHE* 3.7 10.5 - - + +
133A GLU 3.2 0.2 - - - -
134A TYR* 1.3 77.4 - - - +
136A ARG* 1.3 58.1 + - - +
138A THR* 3.4 1.9 + - - -
139A SER* 2.8 34.3 + - - -
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Residues in contact with ARG 136 (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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122A PHE 3.6 16.6 - - - +
123A LEU* 4.1 17.9 - - + +
125A THR* 2.9 47.6 + - - -
126A VAL* 3.9 3.2 + - - +
127A SER 3.0 30.5 + - - -
128A LYS* 4.3 5.5 - - - +
132A PHE* 2.8 24.6 + - - +
133A GLU* 2.8 37.0 + - - +
135A LEU* 1.3 74.4 - - - +
137A LEU* 1.3 56.9 + - - +
139A SER* 3.3 6.3 + - - -
140A LEU* 2.9 38.7 + - + +
170A ILE* 4.6 13.2 - - + -
178A SER* 4.8 7.7 + - - +
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Residues in contact with LEU 137 (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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133A GLU* 2.8 36.7 + - - +
136A ARG* 1.3 73.7 - - - +
138A THR* 1.3 56.8 + - - +
140A LEU* 3.3 8.1 + - + +
141A GLY 3.0 23.6 + - - -
177A LEU* 3.9 20.9 - - + +
178A SER* 3.4 37.5 - - - +
181A VAL* 5.2 0.4 - - + -
798B MET* 3.7 29.2 - - + +
801B LEU* 3.6 20.2 - - + -
805B LEU* 3.7 27.6 - - + +
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Residues in contact with THR 138 (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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91A CYS* 3.5 29.6 - - + +
94A LEU* 3.7 30.1 - - + -
95A ALA* 4.7 4.9 - - + +
98A GLN* 4.7 3.8 - - - +
134A TYR* 2.7 27.0 + - - -
135A LEU 3.8 1.1 - - - -
137A LEU* 1.3 76.7 - - - +
139A SER* 1.3 62.6 + - - +
141A GLY* 3.1 9.9 + - - -
142A VAL* 3.2 14.7 + - + +
801B LEU* 3.3 26.4 - - + +
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Residues in contact with SER 139 (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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94A LEU* 3.6 8.0 - - - +
119A LEU* 3.7 23.5 - - - +
122A PHE* 3.3 28.1 - - - +
123A LEU* 4.0 16.8 - - - -
135A LEU 2.8 22.3 + - - -
136A ARG 3.7 3.6 - - - -
138A THR* 1.3 77.6 - - - +
140A LEU* 1.3 62.2 + - - +
142A VAL* 3.1 14.1 + - - +
143A ILE* 3.2 17.0 + - - +
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Residues in contact with LEU 140 (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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123A LEU* 4.0 22.0 - - + -
136A ARG* 2.9 25.0 + - + +
137A LEU* 3.6 7.9 - - + +
139A SER* 1.3 75.0 - - - +
141A GLY* 1.3 51.2 + - - +
143A ILE* 3.2 4.8 + - - +
144A GLY* 2.7 32.7 + - - -
167A CYS* 5.5 3.1 - - - -
170A ILE* 4.2 19.7 - - + -
178A SER* 4.0 41.7 - - - +
181A VAL* 3.7 20.0 - - + +
182A ALA* 4.4 11.9 - - + +
185A ILE* 3.8 23.3 - - + +
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Residues in contact with GLY 141 (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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98A GLN* 3.6 12.6 - - - -
137A LEU 3.0 11.7 + - - -
138A THR* 3.1 4.9 + - - -
140A LEU* 1.3 73.9 - - - +
142A VAL* 1.3 59.2 + - - +
144A GLY* 4.3 1.3 - - - -
145A ALA* 2.8 32.6 + - - +
181A VAL* 4.9 0.7 - - - -
804B ASN* 5.2 0.4 - - - -
805B LEU* 3.5 25.1 - - - +
808B ILE* 3.7 7.3 - - - +
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Residues in contact with VAL 142 (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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94A LEU* 3.6 32.8 - - + +
97A LEU* 4.5 3.8 - - + -
98A GLN* 3.8 28.9 - - + +
101A ALA* 4.4 3.7 - - + +
110A PHE* 4.4 22.2 - - + -
116A PRO* 6.0 0.2 - - + -
119A LEU* 3.6 24.9 - - + -
138A THR* 3.2 15.5 + - + +
139A SER 3.1 5.8 + - - +
141A GLY* 1.3 75.7 - - - +
143A ILE* 1.3 67.0 + - + +
145A ALA* 3.5 2.4 + - - +
146A LEU* 3.1 21.7 + - - +
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Residues in contact with ILE 143 (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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116A PRO* 3.8 33.0 - - + +
119A LEU* 4.3 15.3 - - + -
120A TYR* 4.6 8.7 - - + -
123A LEU* 5.0 13.5 - - + -
139A SER 3.6 12.6 - - - +
140A LEU* 3.2 7.2 + - - +
142A VAL* 1.3 77.3 - - + +
144A GLY* 1.3 66.6 + - - +
146A LEU* 3.2 9.5 + - + +
147A VAL* 3.0 28.7 + - + +
158A LEU* 4.7 11.2 - - + -
163A ILE* 4.5 9.9 - - + -
185A ILE* 3.7 32.3 - - + -
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Residues in contact with GLY 144 (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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140A LEU 2.7 21.2 + - - -
141A GLY* 3.2 2.0 + - - -
143A ILE* 1.3 72.8 - - - +
145A ALA* 1.3 55.2 + - - +
147A VAL* 3.3 11.7 - - - +
148A LYS* 3.0 29.5 + - - +
181A VAL* 4.9 2.7 - - - -
184A PHE* 3.7 7.8 - - - -
185A ILE* 4.2 9.6 - - - +
808B ILE* 3.6 16.8 - - - -
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Residues in contact with ALA 145 (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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98A GLN* 3.7 30.3 - - + +
101A ALA* 5.5 0.2 - - + -
102A SER* 4.4 19.4 - - - +
141A GLY 2.8 20.3 + - - +
142A VAL 3.9 1.8 - - - +
144A GLY* 1.3 72.3 - - - -
146A LEU* 1.3 62.4 + - - +
148A LYS* 3.4 16.2 + - - +
149A THR* 3.4 16.1 - - - +
808B ILE* 3.8 11.7 - - + +
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Residues in contact with LEU 146 (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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101A ALA* 3.4 36.7 - - + +
107A ARG* 5.0 4.3 - - + -
110A PHE* 4.0 7.9 - - + -
111A LEU* 3.7 26.7 - - + -
116A PRO* 3.7 31.0 - - + -
142A VAL 3.1 17.8 + - - +
143A ILE* 3.2 12.8 + - + +
145A ALA* 1.3 78.5 - - - +
147A VAL* 1.3 57.8 + - - +
149A THR* 3.1 23.0 + - - +
154A VAL* 3.6 27.9 - - + +
158A LEU* 5.0 8.7 - - + -
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Residues in contact with VAL 147 (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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143A ILE* 3.0 19.5 + - + +
144A GLY* 3.3 19.1 - - - +
146A LEU* 1.3 73.8 - - + +
148A LYS* 1.3 63.1 + - - +
149A THR 3.1 4.0 + - - -
150A ASP* 3.2 11.3 + - - -
151A GLU 5.0 0.7 + - - -
154A VAL* 3.8 12.8 - - + -
155A ILE* 4.2 10.1 - - + +
158A LEU* 3.5 31.0 - - + -
184A PHE* 3.9 7.0 - - + -
185A ILE* 4.4 13.0 - - + +
188A LYS* 3.5 41.3 - - + +
189A ILE* 5.4 0.2 - - + -
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Residues in contact with LYS 148 (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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144A GLY 3.0 18.0 + - - +
145A ALA* 3.7 9.2 - - - +
146A LEU 3.3 1.2 - - - -
147A VAL* 1.3 76.4 - - - +
149A THR* 1.3 57.0 + - + +
150A ASP* 3.1 13.1 + - - +
184A PHE* 4.3 15.8 - - + -
188A LYS* 4.5 6.7 + - - +
807B ASP 3.6 14.5 + - - -
808B ILE* 3.0 38.7 + - + +
810B ASP* 4.1 12.5 + - - -
234C ARG* 4.7 17.4 - - - +
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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