Contacts of the helix formed by residues 122 - 139 (chain B) in PDB entry 3GSB
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 SER 122 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ASN* 4.9 8.3 - - - -
125A GLU* 2.6 29.8 + - - -
306A LEU* 6.5 0.4 - - - -
120B VAL* 3.3 9.4 - - - +
121B ASN* 1.3 80.1 - - - +
123B GLY* 1.3 64.4 + - - +
124B THR 3.4 1.2 + - - -
125B GLU* 3.0 21.2 + - - +
126B ALA* 3.1 18.4 + - - +
281B VAL 3.8 8.8 - - - +
282B GLY* 4.1 6.5 - - - -
601B PMP 3.4 14.6 - - - -
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Residues in contact with GLY 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B SER* 1.3 68.2 - - - +
124B THR* 1.3 55.3 + - - +
126B ALA* 3.2 3.5 + - - +
127B CYS* 2.8 41.2 + - - -
247B VAL* 4.0 24.7 - - - -
271B LEU 4.3 7.4 - - - -
272B GLY* 5.1 1.0 - - - -
281B VAL 4.5 2.4 + - - -
282B GLY* 4.6 0.2 - - - -
601B PMP 2.9 25.3 + - - -
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Residues in contact with THR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLU* 3.9 6.1 - - + +
128A MET* 3.9 25.1 - - + -
122B SER* 3.6 5.2 - - - -
123B GLY* 1.3 76.0 - - - +
125B GLU* 1.3 64.4 + - - +
127B CYS* 2.9 12.6 + - - +
128B MET* 2.9 17.9 + - + +
152B GLY* 3.8 16.9 - - - -
153B HIS* 2.8 47.8 + - + +
154B ALA* 4.9 1.1 - - + +
601B PMP 2.7 27.1 + - - -
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A SER* 2.8 32.7 + - - -
124A THR* 4.2 13.1 - - + -
125A GLU* 4.1 12.0 - - + +
153A HIS* 4.8 13.9 + - - +
600A PMP 4.4 2.3 + - - -
120B VAL* 3.5 14.6 - - + +
121B ASN* 3.0 36.1 + - - +
122B SER* 3.0 20.9 + - - +
124B THR* 1.3 79.6 - - - +
126B ALA* 1.3 62.7 + - - +
128B MET* 3.2 19.8 + - - +
129B ALA* 3.0 24.2 + - - +
303B ALA 4.9 4.6 - - - +
304B GLY* 5.5 1.4 - - - -
307B SER* 5.0 0.5 + - - -
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B VAL* 3.7 10.7 - - + +
122B SER 3.1 13.1 + - - +
123B GLY* 3.6 9.2 - - - +
125B GLU* 1.3 77.5 - - - +
127B CYS* 1.3 57.4 - - - +
129B ALA* 3.8 0.9 - - - +
130B VAL* 3.1 30.7 + - - +
270B THR* 3.9 10.9 - - - +
271B LEU 4.5 0.9 - - - +
283B ALA 3.6 28.9 - - - +
284B TYR* 4.0 16.6 - - + +
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Residues in contact with CYS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLY 2.8 19.9 + - - +
124B THR* 2.9 4.7 + - - +
126B ALA* 1.3 75.8 - - - +
128B MET* 1.3 67.1 + - - +
129B ALA 3.3 0.2 + - - -
130B VAL* 3.4 19.6 - - + +
131B LEU* 3.4 14.6 - - + +
151B HIS* 2.8 37.0 - - + +
152B GLY* 4.5 0.2 - - - -
154B ALA* 5.9 1.6 - - + -
210B ILE* 5.1 3.8 - - + -
245B ASP* 3.3 28.5 - - - -
247B VAL* 4.8 0.4 - - - -
270B THR* 4.0 19.1 - - - -
601B PMP 4.1 4.5 - - - -
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Residues in contact with MET 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A THR* 3.7 24.0 - - + -
125A GLU* 6.0 0.4 - - - -
128A MET* 3.4 41.1 - - + +
153A HIS* 4.2 10.3 - - + +
154A ALA* 3.5 29.2 - - + +
155A ASP* 4.9 4.9 - - - +
124B THR* 2.9 14.2 + - - +
125B GLU* 3.4 22.4 - - - +
127B CYS* 1.3 76.4 - - - +
129B ALA* 1.3 64.8 + - + +
131B LEU* 3.4 9.0 + - - +
132B ARG* 3.2 31.5 + - - +
154B ALA* 4.4 15.6 - - + +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A HIS* 5.4 0.9 - - - +
125B GLU 3.0 13.6 + - - +
126B ALA 3.8 2.5 - - - +
128B MET* 1.3 82.1 - - - +
130B VAL* 1.3 57.4 + - - +
132B ARG* 3.3 14.2 + - - +
133B LEU* 2.8 29.9 + - - +
284B TYR* 3.5 38.1 - - + +
300B MET* 4.3 5.3 - - + +
302B GLN* 4.2 13.9 - - + -
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ALA 3.1 14.9 + - - +
127B CYS* 3.4 15.3 - - - +
129B ALA* 1.3 71.7 - - - +
131B LEU* 1.3 61.9 + - + +
133B LEU* 3.6 4.7 - - - +
134B MET* 2.7 39.2 + - - +
210B ILE* 4.2 18.4 - - + -
243B VAL* 3.6 21.5 - - + -
268B LEU* 3.6 30.9 - - + +
269B THR 5.2 0.4 - - - +
270B THR* 3.9 19.7 - - + -
284B TYR* 4.9 12.1 - - + -
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B CYS* 3.4 17.5 - - + +
128B MET* 3.4 10.0 + - - +
129B ALA 3.3 0.6 - - - -
130B VAL* 1.3 81.7 - - + +
132B ARG* 1.3 58.1 + - - +
134B MET* 3.1 25.5 + - - +
135B ARG* 2.8 45.8 + - - +
143B ILE* 4.2 8.5 - - + -
151B HIS 5.8 1.6 - - - +
154B ALA* 5.8 5.2 - - + -
156B MET* 4.4 13.7 - - + -
157B PHE* 3.4 55.4 - - + +
210B ILE* 4.1 10.1 - - + -
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A HIS* 2.7 53.3 + - - -
154A ALA* 4.4 0.8 - - - +
155A ASP* 2.6 42.9 + - - +
158A LEU* 3.5 9.6 - - - +
173A SER 5.0 2.2 + - - -
174A PRO 4.0 6.1 - - - +
175A GLY* 3.4 28.8 - - - -
176A VAL* 3.8 20.6 - - - -
128B MET* 3.2 17.5 + - - +
129B ALA* 3.3 12.2 + - - +
131B LEU* 1.3 77.8 - - - +
133B LEU* 1.3 55.8 + - - +
135B ARG* 3.4 1.7 + - - +
136B ALA* 2.8 32.1 + - - +
300B MET* 4.2 13.3 - - + +
301B TYR 3.1 21.0 + - - -
302B GLN* 4.2 5.3 - - - +
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ALA 2.8 18.9 + - - +
130B VAL* 3.6 6.3 - - - +
132B ARG* 1.3 76.2 - - - +
134B MET* 1.3 60.0 + - - +
136B ALA* 3.7 1.3 - - + -
137B TYR* 2.8 29.6 + - - +
268B LEU* 3.9 16.2 - - + -
284B TYR* 4.8 8.3 - - + -
290B ILE* 3.7 38.4 - - + +
291B MET* 4.0 22.0 - - - -
293B LEU* 4.1 17.3 - - + -
294B VAL* 4.0 15.7 - - + -
300B MET* 3.7 22.3 - - + -
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Residues in contact with MET 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B VAL* 2.7 21.3 + - - +
131B LEU* 3.2 36.1 - - - +
133B LEU* 1.3 72.7 - - - +
135B ARG* 1.3 62.6 + - - +
137B TYR* 3.7 1.6 - - - +
138B THR* 3.0 29.2 + - - +
143B ILE* 3.8 19.7 - - + -
207B ALA* 4.1 3.1 - - - -
208B GLY* 3.4 43.3 - - - +
209B VAL 3.8 2.2 - - - +
210B ILE* 4.7 6.1 - - - -
241B LEU* 3.8 24.9 - - + +
243B VAL* 3.5 34.5 - - + -
268B LEU* 4.8 4.0 - - + -
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Residues in contact with ARG 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ASP* 4.7 4.8 + - - -
175A GLY* 3.3 27.0 + - - +
177A PRO* 3.7 18.1 - - - +
131B LEU* 2.8 30.3 + - - +
132B ARG* 3.8 0.8 - - - +
134B MET* 1.3 75.5 - - - +
136B ALA* 1.3 56.7 + - - +
138B THR* 4.0 0.7 - - - -
139B GLY* 2.8 31.2 + - - -
140B ARG 3.2 19.2 + - - +
141B ASP* 2.8 46.5 + - - +
143B ILE* 3.3 31.5 - - + +
156B MET* 3.1 54.3 - - - +
183B ASN* 3.6 2.8 - - - +
184B THR* 5.2 0.4 - - - +
207B ALA* 4.1 0.9 - - - -
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Residues in contact with ALA 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A PRO* 3.2 30.1 - - + +
175A GLY* 3.5 7.7 - - - +
132B ARG 2.8 22.3 + - - +
133B LEU* 3.7 6.5 - - + +
135B ARG* 1.3 75.6 - - - +
137B TYR* 1.3 62.9 + - - +
138B THR 4.3 0.2 - - - -
139B GLY* 3.7 7.0 + - - -
293B LEU* 4.2 14.7 - - + +
300B MET* 4.7 5.6 - - + -
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Residues in contact with TYR 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LEU 2.8 20.9 + - - +
134B MET 3.7 3.8 - - - +
136B ALA* 1.3 77.2 - - - +
138B THR* 1.3 67.9 + - + +
241B LEU* 3.9 26.2 - - + -
289B GLU* 4.2 16.9 - - + +
290B ILE* 3.7 53.1 - - + +
293B LEU* 3.8 22.0 - - + +
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Residues in contact with THR 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B MET 3.0 16.5 + - - +
135B ARG 3.5 0.2 + - - -
137B TYR* 1.3 88.9 - - + +
139B GLY* 1.3 62.8 + - - +
140B ARG* 3.4 41.8 + - - +
207B ALA* 3.4 33.5 - - - +
239B ASP 4.3 6.7 - - - +
241B LEU* 3.9 17.0 - - + +
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Residues in contact with GLY 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ARG 2.8 13.3 + - - -
136B ALA* 3.7 5.4 + - - -
137B TYR 3.5 1.4 - - - -
138B THR* 1.3 80.1 - - - +
140B ARG* 1.3 62.6 + - - +
141B ASP* 4.4 5.0 - - - +
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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
------------------------------------------------------------
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