Contacts of the helix formed by residues 131 - 143 (chain B) in PDB entry 4HYY
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 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ARG* 5.8 0.7 - - - -
130B THR* 1.3 74.6 - - - +
132B LYS* 1.3 65.0 + - - +
133B THR 3.1 2.5 - - - -
134B GLN* 3.9 15.3 - - - +
135B LEU* 2.9 25.6 + - - +
303B LEU* 3.9 8.2 - - - +
311B ARG* 2.7 23.9 - - - +
328B PHE* 5.3 5.9 - - - -
330B ILE* 5.0 4.3 - - - -
335B ILE* 4.4 2.8 - - - +
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Residues in contact with LYS 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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124B ALA* 3.9 18.2 - - - +
125B PHE* 4.5 3.6 - - - -
126B GLY 3.3 25.8 + - - +
127B GLU 3.7 14.9 + - - -
128B PHE 5.2 3.4 + - - -
129B ARG* 5.6 0.4 - - - +
130B THR* 2.8 15.5 + - - +
131B GLY* 1.3 78.6 - - - +
133B THR* 1.3 62.4 + - - +
135B LEU* 3.2 5.6 + - - +
136B SER* 2.9 30.6 + - - -
223B ASP* 5.2 0.4 - - - +
265B PHE* 4.3 1.3 - - - -
267B THR* 3.7 24.2 - - + +
268B ASN 3.6 20.2 - - - +
269B GLN* 4.3 18.8 - - + +
303B LEU* 3.7 17.1 - - + +
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Residues in contact with THR 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B THR 4.0 4.1 + - - -
131B GLY 3.1 0.2 - - - -
132B LYS* 1.3 79.7 - - - +
134B GLN* 1.3 67.7 + - - +
135B LEU 3.2 0.9 - - - -
136B SER* 3.3 6.8 + - - -
137B HIS* 2.8 54.7 + - + -
162B GLU* 5.6 1.0 - - - +
164B THR* 4.2 19.7 + - + +
223B ASP* 3.2 23.4 + - - +
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Residues in contact with GLN 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG* 5.0 11.9 - - - +
131B GLY* 3.5 12.1 + - - +
132B LYS 3.5 0.2 - - - -
133B THR* 1.3 85.4 - - + +
135B LEU* 1.3 56.1 + - - +
137B HIS* 3.6 7.7 + - - +
138B THR* 2.7 33.6 + - - -
169B ARG* 3.0 43.5 + - - +
173B ILE* 5.4 0.4 - - - +
330B ILE* 4.4 16.7 - - + +
331B THR 3.9 13.9 + - - +
334B GLY* 4.2 8.5 - - - -
335B ILE* 3.7 17.5 - - + +
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Residues in contact with LEU 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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103B THR* 4.2 27.1 - - + +
108B PHE* 4.0 27.1 - - + -
116B ILE* 5.4 2.2 - - + -
124B ALA* 4.8 7.0 - - + -
131B GLY 2.9 19.3 + - - +
132B LYS 3.4 5.6 - - - +
133B THR 3.2 0.2 - - - -
134B GLN* 1.3 73.4 - - - +
136B SER* 1.3 68.7 + - - +
138B THR* 2.9 11.5 + - - -
139B LEU* 2.9 38.3 + - + +
265B PHE* 3.5 28.0 - - + -
301B ILE* 6.1 0.9 - - + -
303B LEU* 5.3 5.4 - - + -
328B PHE* 6.1 0.7 - - + -
335B ILE* 3.7 19.0 - - + +
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Residues in contact with SER 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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132B LYS 2.9 15.6 + - - -
133B THR* 3.4 10.5 - - - -
135B LEU* 1.3 77.7 - - - +
137B HIS* 1.3 66.2 + - - +
139B LEU 3.2 6.8 + - - -
140B CYS* 3.4 14.6 + - - -
158B PHE* 3.9 27.6 - - - -
221B ILE* 3.7 14.0 - - - +
223B ASP* 3.7 15.1 + - - +
265B PHE* 3.8 11.7 - - - -
267B THR* 3.8 11.8 - - - +
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Residues in contact with HIS 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 THR* 2.8 50.6 + - + +
134B GLN* 4.2 8.2 + - - +
136B SER* 1.3 79.0 - - - +
138B THR* 1.3 63.5 + - - +
140B CYS* 3.2 10.8 + - - +
141B VAL* 3.8 1.9 + - - +
158B PHE* 5.2 2.5 - + - -
164B THR 3.5 12.8 + - - -
165B PHE* 3.6 21.8 - + - -
166B ARG* 3.0 44.7 + - + +
169B ARG* 4.0 18.8 - - + +
170B LEU* 3.2 30.9 - - + +
173B ILE* 4.3 13.4 - - + +
223B ASP* 5.6 0.4 - - - -
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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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103B THR 3.4 26.2 - - - +
134B GLN 2.7 22.4 + - - -
135B LEU* 2.9 7.1 + - - -
137B HIS* 1.3 77.7 - - - +
139B LEU* 1.3 62.8 + - - +
141B VAL* 3.1 6.9 + - - +
142B THR* 3.0 31.7 + - + -
173B ILE* 4.2 16.0 - - + +
176B ARG* 4.5 7.0 - - - +
334B GLY* 3.5 7.6 - - - -
335B ILE* 3.0 32.4 + - + +
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Residues in contact with LEU 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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101B ILE* 3.9 11.2 - - + +
102B THR 3.6 22.2 - - - +
103B THR* 4.3 7.2 - - - -
116B ILE* 3.6 27.1 - - + -
135B LEU* 2.9 36.4 + - + +
136B SER* 3.2 4.7 + - - +
138B THR* 1.3 72.8 - - - +
140B CYS* 1.3 64.3 + - - +
141B VAL 3.0 2.0 - - - -
142B THR* 3.5 4.9 - - - +
143B ALA* 3.0 30.7 + - - +
219B LEU* 3.6 20.3 - - + +
221B ILE* 4.3 0.9 - - + -
265B PHE* 3.8 35.4 - - + -
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Residues in contact with CYS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B SER 3.4 12.7 + - - -
137B HIS* 3.2 11.8 + - - +
139B LEU* 1.3 76.2 - - - +
141B VAL* 1.3 58.5 + - - +
144B GLN* 3.0 29.8 + - - +
156B ILE* 3.5 15.3 - - - +
158B PHE* 3.5 34.1 - - - -
165B PHE* 4.2 12.8 - - - -
170B LEU* 3.7 17.9 - - + -
184B VAL* 4.4 0.2 - - - +
188B VAL* 3.9 13.1 - - + +
221B ILE* 4.0 5.2 - - - -
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B HIS 4.3 0.9 - - - +
138B THR 3.1 6.7 + - - +
139B LEU 3.0 0.4 - - - -
140B CYS* 1.3 79.2 - - - +
142B THR* 1.3 60.0 + - - +
143B ALA 3.2 2.0 - - - -
144B GLN* 2.8 30.8 + - - +
145B LEU* 3.6 11.2 - - + +
170B LEU* 4.0 25.4 - - + +
173B ILE* 3.7 22.2 - - + -
174B ALA* 4.3 13.7 - - - +
177B PHE* 3.9 26.9 - - + -
179B VAL* 6.0 0.7 - - + -
184B VAL* 4.0 26.9 - - + -
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Residues in contact with THR 142 (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 ILE* 3.7 7.1 - - - +
102B THR* 2.8 44.0 + - + +
104B GLY 4.5 4.5 - - - +
138B THR* 3.0 27.2 + - + +
139B LEU* 3.5 9.7 - - - -
141B VAL* 1.3 75.8 - - - +
143B ALA* 1.3 61.8 + - - +
144B GLN 3.1 0.2 - - - -
145B LEU* 3.3 28.5 + - + +
151B TYR* 4.5 1.6 - - - -
177B PHE* 3.6 35.7 - - + -
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Residues in contact with ALA 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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101B ILE* 3.6 23.6 - - + -
139B LEU 3.0 19.8 + - - +
142B THR* 1.3 78.1 + - - +
144B GLN* 1.3 57.7 + - - +
145B LEU 3.3 0.4 - - - -
151B TYR* 2.7 30.0 + - - +
153B GLY* 3.3 2.6 - - - -
154B GLY 3.0 16.6 + - - +
156B ILE* 3.6 21.5 - - + -
218B LYS* 5.1 1.8 - - + -
219B LEU* 4.1 4.5 - - + -
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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