Contacts of the helix formed by residues 122 - 139 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A VAL* 3.5 7.9 - - - +
121A ASN* 1.3 80.2 - - - +
123A GLY* 1.3 65.1 + - - +
124A THR 3.4 9.0 + - - -
125A GLU* 3.1 10.8 + - - +
126A ALA* 3.0 18.7 + - - +
281A VAL 4.1 4.3 - - - +
282A GLY* 3.6 13.9 - - - +
600A PMP 3.5 12.2 + - - -
121B ASN* 4.8 7.9 - - - -
125B GLU* 2.8 28.0 + - - -
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Residues in contact with GLY 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A SER* 1.3 73.5 - - - +
124A THR* 1.3 57.0 + - - +
126A ALA* 3.0 6.1 + - - +
127A CYS* 2.9 36.4 + - - +
247A VAL* 3.8 24.9 - - - -
271A LEU 4.6 1.1 - - - -
272A GLY* 5.0 1.2 - - - -
281A VAL 4.8 1.2 + - - -
282A GLY* 4.5 1.2 - - - -
600A PMP 3.0 27.7 + - - -
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Residues in contact with THR 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A SER* 3.3 4.9 - - - -
123A GLY* 1.3 76.3 - - - +
125A GLU* 1.3 61.1 + - - +
127A CYS* 4.1 1.0 - - - +
128A MET* 3.1 22.7 + - - +
150A TYR* 4.9 0.5 + - - -
151A HIS 4.6 2.0 - - - +
152A GLY* 3.4 25.4 - - - -
153A HIS* 3.8 31.0 + - + +
154A ALA* 4.8 2.7 - - - +
600A PMP 3.2 21.0 + - - -
125B GLU* 4.2 9.6 - - + +
128B MET* 3.7 31.6 - - + -
303B ALA 5.0 1.0 + - - -
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A VAL* 3.3 21.5 - - + +
121A ASN* 2.8 40.2 + - - +
122A SER* 3.1 16.8 + - - +
124A THR* 1.3 75.9 - - + +
126A ALA* 1.3 60.9 + - - +
128A MET* 3.3 16.3 + - + +
129A ALA* 2.9 31.0 + - - +
307A SER* 5.1 0.2 + - - -
122B SER* 2.6 34.0 + - - -
124B THR* 3.9 9.6 + - + -
125B GLU* 4.3 10.5 - - + +
153B HIS* 4.7 14.0 + - - +
601B PMP 4.3 0.9 + - - -
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Residues in contact with ALA 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A VAL* 3.5 10.2 - - + +
122A SER 3.0 12.4 + - - +
123A GLY* 3.0 8.6 + - - +
125A GLU* 1.3 76.8 - - - +
127A CYS* 1.3 57.3 + - - +
129A ALA* 3.3 2.9 + - - +
130A VAL* 3.0 30.3 + - - +
270A THR* 3.8 10.6 - - - +
271A LEU 4.1 5.6 - - - +
283A ALA 3.2 36.3 - - - +
284A TYR* 3.9 9.2 - - + +
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Residues in contact with CYS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLY 2.9 17.8 + - - +
124A THR 4.3 1.1 - - - +
126A ALA* 1.3 75.8 - - - +
128A MET* 1.3 57.7 + - - +
130A VAL* 3.0 11.9 - - + +
131A LEU* 2.9 28.2 + - - +
151A HIS* 3.1 32.5 - - + +
157A PHE* 3.8 12.8 - - + -
210A ILE* 5.0 2.9 - - + -
245A ASP* 3.6 28.9 - - - -
247A VAL* 4.9 1.1 - - - -
270A THR* 3.8 20.9 - - - -
600A PMP 4.6 2.2 - - - -
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Residues in contact with MET 128 (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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124A THR 3.1 20.2 + - - +
125A GLU* 3.7 14.1 - - + +
126A ALA 3.3 0.2 - - - -
127A CYS* 1.3 78.1 - - - +
129A ALA* 1.3 59.9 + - - +
131A LEU* 3.2 21.5 + - + +
132A ARG* 3.3 15.6 + - - +
154A ALA* 4.1 13.5 - - + -
157A PHE* 4.4 5.5 - - - -
124B THR* 3.9 20.9 - - + -
128B MET* 3.4 35.2 - - + +
153B HIS* 3.6 28.9 - - + +
154B ALA* 4.6 6.7 - - - -
155B ASP* 4.1 19.1 - - - +
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A VAL* 5.7 0.2 - - + -
125A GLU 2.9 16.8 + - - +
126A ALA 3.7 1.6 - - - +
127A CYS 3.2 0.2 - - - -
128A MET* 1.3 76.6 - - - +
130A VAL* 1.3 58.9 + - - +
132A ARG* 3.5 11.3 + - - +
133A LEU* 3.0 28.0 + - - +
284A TYR* 3.4 36.6 - - + +
300A MET* 3.9 7.8 - - + +
302A GLN* 4.2 17.9 - - + -
153B HIS* 6.1 0.4 - - + -
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ALA 3.0 14.2 + - - +
127A CYS* 3.0 25.1 - - - +
129A ALA* 1.3 73.7 - - - +
131A LEU* 1.3 67.9 + - - +
133A LEU* 3.8 5.1 - - + +
134A MET* 3.0 27.7 + - + +
210A ILE* 4.5 11.0 - - + -
243A VAL* 4.0 17.0 - - + -
268A LEU* 3.6 39.5 - - + -
269A THR 5.3 0.7 - - - +
270A THR* 3.9 16.4 - - + -
284A TYR* 4.6 14.3 - - + -
285A GLY 5.9 0.2 - - - +
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Residues in contact with LEU 131 (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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127A CYS 2.9 13.1 + - - +
128A MET* 3.2 13.2 - - + +
129A ALA 3.2 0.2 - - - -
130A VAL* 1.3 76.0 - - - +
132A ARG* 1.3 67.2 + - + +
134A MET* 3.0 25.9 + - - +
135A ARG* 3.4 16.8 + - + +
143A ILE* 4.0 28.9 - - + -
154A ALA* 5.3 4.9 - - + -
156A MET* 3.8 41.7 - - + +
157A PHE* 3.5 32.3 - - + -
155B ASP* 5.6 6.1 - - - +
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Residues in contact with ARG 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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128A MET* 3.6 17.4 - - - +
129A ALA* 3.6 9.7 - - - +
131A LEU* 1.3 81.2 - - + +
133A LEU* 1.3 64.2 + - - +
135A ARG* 3.0 18.0 + - - +
136A ALA* 3.0 12.6 + - - +
300A MET* 3.7 15.0 - - - +
301A TYR 2.5 30.8 + - - -
302A GLN* 4.1 13.1 - - - +
153B HIS* 3.9 23.2 + - - -
154B ALA 5.2 1.3 - - - -
155B ASP* 3.6 28.5 - - - +
158B LEU* 3.9 14.9 - - - +
173B SER 4.1 0.6 + - - -
174B PRO* 2.5 37.8 + - - +
175B GLY* 3.6 23.2 - - - +
176B VAL* 3.8 10.1 - - - +
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Residues in contact with LEU 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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129A ALA 3.0 14.2 + - - +
130A VAL* 3.8 6.7 - - - +
132A ARG* 1.3 77.6 - - - +
134A MET* 1.3 64.1 + - - +
136A ALA* 4.3 2.0 - - + -
137A TYR* 2.8 27.6 + - - +
268A LEU* 4.5 12.6 - - + -
284A TYR* 4.3 10.8 - - + -
290A ILE* 3.8 35.9 - - + +
291A MET* 4.1 23.3 - - - -
293A LEU* 4.0 16.8 - - + -
294A VAL* 3.7 21.5 - - + -
300A MET* 3.4 22.0 - - + -
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Residues in contact with MET 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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130A VAL* 3.0 26.4 + - + +
131A LEU* 3.0 14.6 + - - +
133A LEU* 1.3 76.8 - - - +
135A ARG* 1.3 64.9 + - + +
137A TYR* 3.4 0.7 + - - +
138A THR* 3.1 30.0 + - - +
143A ILE* 3.2 25.6 - - + -
207A ALA* 3.8 9.4 - - + +
208A GLY* 3.1 40.6 - - - +
210A ILE* 5.2 8.1 - - - -
241A LEU* 3.9 16.8 - - + -
243A VAL* 3.8 32.1 - - + -
268A LEU* 4.6 8.3 - - + +
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Residues in contact with ARG 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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131A LEU* 3.9 24.6 + - + +
132A ARG* 3.0 8.1 + - - +
134A MET* 1.3 75.6 - - + +
136A ALA* 1.3 57.6 + - - +
137A TYR 3.2 0.2 + - - -
138A THR* 4.1 0.9 - - - -
139A GLY* 2.7 36.6 + - - -
140A ARG 3.5 19.6 + - - +
141A ASP* 3.3 34.1 + - - +
143A ILE* 5.2 2.0 - - + -
156A MET* 3.0 38.0 - - - +
183A ASN* 4.3 7.9 - - - +
207A ALA* 4.9 3.4 - - + -
155B ASP* 3.5 17.2 + - - -
175B GLY 3.7 9.5 + - - +
177B PRO* 3.0 42.5 - - + +
180B THR* 4.3 5.3 - - - +
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Residues in contact with ALA 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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132A ARG 3.0 14.2 + - - +
133A LEU* 3.8 7.6 - - - +
135A ARG* 1.3 76.5 - - - +
137A TYR* 1.3 62.4 + - - +
138A THR 3.6 0.2 + - - -
139A GLY* 3.9 4.9 + - - -
293A LEU* 3.8 17.8 - - + +
299A PRO* 6.5 0.4 - - + -
300A MET* 4.7 11.4 - - + -
175B GLY* 4.4 18.7 - - - +
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Residues in contact with TYR 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 LEU* 2.8 18.0 + - + +
134A MET 3.7 2.7 - - - +
136A ALA* 1.3 80.7 - - - +
138A THR* 1.3 66.9 + - + +
241A LEU* 3.7 32.5 - - + -
289A GLU* 3.9 27.0 - - + +
290A ILE* 3.8 35.7 - - + +
293A LEU* 3.6 21.9 - - + +
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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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134A MET 3.1 18.3 + - - +
135A ARG 3.7 0.2 + - - -
137A TYR* 1.3 93.1 - - + +
139A GLY* 1.3 63.5 + - - +
140A ARG* 3.2 23.7 + - - +
207A ALA* 3.2 41.3 - - - +
239A ASP 4.6 12.1 - - - +
241A LEU* 3.9 12.6 - - + -
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Residues in contact with GLY 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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135A ARG 2.7 18.2 + - - -
136A ALA 3.9 4.2 + - - -
137A TYR 3.5 2.0 - - - -
138A THR* 1.3 74.6 - - - +
140A ARG* 1.3 61.8 + - - +
141A ASP* 4.4 1.0 + - - +
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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
------------------------------------------------------------
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