Contacts of the helix formed by residues 134 - 150 (chain B) in PDB entry 1W5B
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 GLY 134 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B ALA* 3.7 8.1 - - - -
99B GLY* 3.6 2.4 - - - -
100B ASN 3.4 32.1 - - - -
101B PRO* 3.3 4.4 - - - +
104B GLY* 3.2 12.8 - - - -
133B GLY* 1.3 74.1 - - - -
135B THR* 1.3 60.0 + - - +
138B GLY 3.1 19.6 + - - -
500B GTP 3.0 14.6 + - - -
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Residues in contact with THR 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLY* 3.7 21.1 - - - +
69B ILE 4.8 0.2 - - - +
70B ASN* 3.8 15.6 + - - +
71B THR* 2.7 40.1 + - + +
87B ILE* 4.7 5.2 - - + -
97B ALA* 3.6 2.1 - - - +
104B GLY* 4.0 6.3 - - - -
134B GLY* 1.3 74.0 - - - +
136B GLY* 1.3 58.1 + - - +
139B SER* 2.6 46.9 + - - +
500B GTP 2.8 29.6 + - - -
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Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B CYS* 3.8 23.8 - - - -
46B GLY* 4.2 0.2 - - - -
129B CYS* 3.8 15.7 - - - -
130B GLY 4.7 2.0 - - - -
135B THR* 1.3 73.6 - - - +
137B THR* 1.3 62.5 + - - +
140B ALA* 3.1 30.5 + - - +
500B GTP 2.8 21.6 + - - -
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Residues in contact with THR 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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101B PRO* 4.0 9.0 - - + -
129B CYS* 4.5 0.2 - - - -
130B GLY 4.7 1.4 + - - -
131B LEU* 3.7 14.4 - - + +
132B GLY 2.8 26.4 + - - +
133B GLY 2.7 26.8 + - - -
135B THR 3.4 0.2 - - - -
136B GLY* 1.3 75.6 - - - +
138B GLY* 1.3 57.2 + - - +
141B PRO* 3.2 20.6 - - - +
172B ASN 3.4 26.2 - - - +
173B ALA* 4.7 0.2 - - - -
176B GLY* 3.7 11.6 - - - -
179B ARG* 3.2 23.6 + - - +
500B GTP 4.5 0.2 + - - -
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Residues in contact with GLY 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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101B PRO* 3.2 28.7 - - - +
105B GLU* 3.2 25.4 - - - +
134B GLY 3.1 10.7 + - - -
137B THR* 1.3 81.5 - - - +
139B SER* 1.3 60.1 + - - +
141B PRO* 3.6 8.7 - - - +
142B VAL* 3.6 6.6 - - - +
179B ARG* 4.3 4.7 + - - -
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Residues in contact with SER 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B CYS* 3.3 21.9 - - - +
69B ILE* 4.6 4.2 - - - +
87B ILE* 4.1 11.7 - - - -
104B GLY 3.7 6.2 + - - -
108B ALA* 3.5 26.5 - - - -
135B THR* 2.6 31.2 + - - +
138B GLY* 1.3 71.2 - - - +
140B ALA* 1.3 66.6 + - - +
141B PRO 3.4 2.5 - - - -
142B VAL* 3.1 5.2 + - - +
143B VAL* 2.9 25.9 + - - +
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Residues in contact with ALA 140 (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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45B CYS* 4.2 8.1 - - - -
127B ILE* 3.9 24.6 - - + +
129B CYS* 4.1 15.7 - - - -
131B LEU* 5.3 1.3 - - + -
136B GLY 3.1 19.2 + - - +
139B SER* 1.3 78.6 + - - +
141B PRO* 1.3 62.0 - - + +
143B VAL* 3.2 3.7 + - - +
144B ALA* 2.9 28.6 + - - +
158B VAL* 5.5 0.2 - - + -
180B LEU* 3.9 15.8 - - + +
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Residues in contact with PRO 141 (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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105B GLU* 6.5 0.4 - - + -
131B LEU* 6.2 0.4 - - + -
137B THR 3.2 17.5 - - - +
138B GLY 3.6 5.4 - - - +
139B SER 3.5 3.4 - - - -
140B ALA* 1.3 93.6 - - + +
142B VAL* 1.3 56.4 - - + +
144B ALA* 3.3 4.0 + - + +
145B GLU* 2.9 28.6 + - - +
176B GLY 4.2 4.0 - - - +
179B ARG* 3.4 51.1 - - + +
180B LEU* 3.8 21.8 - - + +
183B HIS* 3.7 8.4 - - + -
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Residues in contact with VAL 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLU* 3.9 20.9 - - + +
108B ALA* 3.6 35.2 - - + +
109B LYS* 4.1 17.3 - - + +
112B ALA* 5.4 1.1 - - + -
115B ILE* 5.1 0.9 - - + -
138B GLY 3.6 19.7 - - - +
139B SER 3.1 6.9 + - - +
141B PRO* 1.3 76.9 - - + +
143B VAL* 1.3 65.6 + - - +
145B GLU* 3.2 8.4 + - + +
146B ILE* 3.0 39.0 + - + +
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Residues in contact with VAL 143 (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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43B VAL* 4.1 21.8 - - + -
45B CYS* 4.1 12.8 - - - -
69B ILE* 3.9 25.4 - - + -
115B ILE* 4.3 27.4 - - + -
119B ILE* 4.3 7.8 - - + +
125B VAL* 5.0 1.1 - - + -
127B ILE* 3.9 20.6 - - + -
139B SER* 2.9 21.5 + - - +
140B ALA* 3.6 7.0 - - - +
142B VAL* 1.3 74.8 - - + +
144B ALA* 1.3 57.8 + - - +
146B ILE* 3.5 3.1 + - - +
147B SER* 2.9 26.2 + - - -
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Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 3.3 19.7 - - + +
140B ALA 2.9 16.7 + - - +
141B PRO* 3.4 9.9 - - + +
143B VAL* 1.3 75.3 - - - +
145B GLU* 1.3 65.2 + - - +
147B SER* 3.0 4.3 + - - -
148B LYS* 3.0 19.1 + - - +
154B THR* 3.9 5.6 - - + +
180B LEU* 4.1 10.8 - - + -
183B HIS* 3.6 29.2 - - + +
184B THR* 4.1 2.2 - - + -
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Residues in contact with GLU 145 (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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141B PRO 2.9 16.5 + - - +
142B VAL* 3.7 8.3 - - - +
144B ALA* 1.3 75.4 - - - +
146B ILE* 1.3 63.6 + - + +
148B LYS* 3.2 6.0 + - - +
149B LYS* 3.0 55.8 + - + +
183B HIS* 3.2 43.5 + - + +
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Residues in contact with ILE 146 (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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112B ALA* 3.7 37.0 - - + +
115B ILE* 3.8 18.2 - - + -
116B LYS* 3.6 37.5 - - + -
119B ILE* 4.1 9.4 - - + -
142B VAL* 3.0 29.6 + - + +
143B VAL* 3.7 4.3 - - - +
145B GLU* 1.3 76.3 - - + +
147B SER* 1.3 62.3 + - - +
149B LYS* 3.3 14.2 + - + +
150B ILE* 3.2 23.6 + - + +
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Residues in contact with SER 147 (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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119B ILE* 3.8 16.8 - - - -
125B VAL* 3.5 26.0 - - - +
127B ILE* 4.9 0.2 - - - -
143B VAL 2.9 15.4 + - - -
144B ALA* 3.0 8.3 + - - -
146B ILE* 1.3 77.6 - - - +
148B LYS* 1.3 58.6 + - - +
150B ILE* 3.0 22.3 - - - +
152B ALA* 3.1 16.3 + - - +
154B THR* 2.5 29.7 + - - -
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Residues in contact with LYS 148 (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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144B ALA 3.0 7.1 + - - +
145B GLU* 3.2 7.4 + - + +
147B SER* 1.3 73.9 - - - +
149B LYS* 1.3 62.0 + - + +
151B GLY* 2.8 21.5 + - - +
152B ALA 4.4 6.2 + - - -
154B THR* 3.4 11.9 - - - +
182B GLN 5.1 1.1 - - - +
183B HIS* 3.0 42.8 - - - +
184B THR 4.3 1.1 - - - +
185B ASP* 2.6 36.3 + - - +
244B ASN* 5.6 0.4 + - - -
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Residues in contact with LYS 149 (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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116B LYS* 5.8 2.7 - - - +
145B GLU* 3.0 48.4 + - + +
146B ILE* 3.3 18.1 + - + +
148B LYS* 1.3 78.7 - - + +
150B ILE* 1.3 59.5 + - + +
151B GLY 3.3 3.1 + - - -
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Residues in contact with ILE 150 (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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116B LYS* 3.7 36.8 - - + +
119B ILE* 3.3 45.1 - - + +
120B GLN* 4.1 22.1 + - - +
121B ASP* 4.3 2.2 + - - +
122B SER* 4.3 8.4 - - - +
125B VAL* 5.0 0.2 - - + -
146B ILE* 3.2 15.0 + - + +
147B SER 3.0 19.1 - - - +
149B LYS* 1.3 76.8 - - + +
151B GLY* 1.3 58.9 + - - +
152B ALA* 3.5 15.9 + - + +
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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