Contacts of the helix formed by residues 136 - 145 (chain B) in PDB entry 3EU9
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 HIS 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A HIS* 5.5 1.6 - + - -
98B ALA 3.7 10.7 + - - +
99B ILE 2.9 29.0 + - - -
100B ASN 4.2 1.6 - - - -
101B ASN* 3.6 36.5 - - + +
131B ALA 3.1 10.3 + - - +
134B GLN* 3.8 24.1 + - + +
135B GLY* 1.3 76.4 - - - +
137B LEU* 1.3 60.0 + - - +
138B SER 3.5 2.7 - - - -
139B MET* 3.2 17.0 + - + +
140B VAL* 3.0 30.7 + - - +
172B ILE* 4.0 0.4 - - - +
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Residues in contact with LEU 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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135B GLY 3.3 7.5 + - - +
136B HIS* 1.3 69.7 - - - +
138B SER* 1.3 68.1 + - - +
140B VAL* 3.1 5.4 + - + +
141B VAL* 2.9 40.5 + - + +
171B SER* 3.9 46.0 - - - +
172B ILE* 4.0 16.8 - - + -
175B TYR* 4.0 21.1 - - + -
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Residues in contact with SER 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 ASN* 4.9 7.9 - - - -
103B ILE* 3.9 13.6 - - - +
136B HIS 3.5 0.4 - - - -
137B LEU* 1.3 79.9 - - - +
139B MET* 1.3 56.5 - - - +
141B VAL* 3.5 8.8 + - - +
142B GLN* 2.9 28.2 + - - +
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Residues in contact with MET 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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97B ALA 3.9 3.6 - - - +
98B ALA* 3.5 13.5 - - - +
101B ASN* 3.7 17.8 - - - +
102B ARG 3.6 13.7 - - - +
103B ILE* 3.3 39.9 - - + +
106B VAL* 3.4 36.1 - - + -
131B ALA* 3.5 21.8 - - + -
136B HIS* 3.2 14.7 + - + +
137B LEU 3.1 0.6 - - - -
138B SER* 1.3 76.9 - - - +
140B VAL* 1.3 60.2 + - - +
141B VAL 3.1 0.2 - - - -
142B GLN* 3.2 1.5 + - - +
143B LEU* 2.8 43.4 + - + +
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Residues in contact with VAL 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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128B LEU* 3.7 21.1 - - + +
131B ALA* 4.1 1.8 - - + -
132B THR* 3.8 37.2 - - - +
136B HIS 3.0 19.6 + - - +
137B LEU* 3.5 9.6 - - + +
139B MET* 1.3 74.7 - - - +
141B VAL* 1.3 62.5 + - - +
144B MET* 3.1 41.6 + - - +
160B CYS* 6.1 0.2 - - - -
172B ILE* 4.1 18.8 - - + -
175B TYR* 4.8 6.3 - - + -
176B LEU* 4.3 14.6 - - + -
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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
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137B LEU* 2.9 33.2 + - + +
138B SER* 3.5 8.3 - - - +
140B VAL* 1.3 75.0 - - - +
142B GLN* 1.3 65.6 + - - +
144B MET* 3.8 2.3 - - - +
145B LYS* 3.0 27.4 + - + +
175B TYR* 3.6 50.3 + - + +
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Residues in contact with GLN 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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103B ILE* 4.0 25.3 - - + +
106B VAL* 4.4 12.3 - - + -
107B LYS* 3.0 29.6 + - + +
138B SER 2.9 18.1 + - - +
139B MET* 3.6 4.9 - - - +
141B VAL* 1.3 76.4 - - - +
143B LEU* 1.3 66.9 + - - +
145B LYS* 3.0 23.2 + - - +
146B TYR* 3.1 46.1 + - + -
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Residues in contact with LEU 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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94B LEU* 4.8 4.9 - - + -
98B ALA* 4.1 3.8 - - + -
106B VAL* 3.6 27.1 - - + -
110B ILE* 4.5 9.2 - - + -
116B VAL* 4.4 9.4 - - + +
127B PRO* 3.8 17.9 - - + +
128B LEU* 3.4 41.3 - - + +
131B ALA* 4.1 0.7 - - + -
139B MET* 2.8 41.0 + - + +
140B VAL 4.0 2.9 - - - +
142B GLN* 1.3 72.3 - - - +
144B MET* 1.3 57.7 + - - +
146B TYR* 2.8 26.2 + - - +
148B ALA* 3.1 23.8 + - + +
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Residues in contact with MET 144 (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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128B LEU* 4.0 13.2 - - + -
140B VAL* 3.1 27.4 + - - +
141B VAL* 3.8 4.3 - - - +
143B LEU* 1.3 73.8 - - - +
145B LYS* 1.3 56.8 + - - +
146B TYR 2.9 10.5 + - - -
147B GLY* 3.0 13.9 + - - -
148B ALA 3.6 20.5 + - - +
150B PRO* 3.8 24.0 - - + -
175B TYR* 4.1 12.1 - - + +
176B LEU* 3.9 23.8 - - + -
179B LYS* 4.1 37.0 - - + -
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Residues in contact with LYS 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 VAL* 3.0 19.0 + - + +
142B GLN* 3.0 25.2 + - - +
144B MET* 1.3 75.3 - - - +
146B TYR* 1.3 65.9 + - + +
147B GLY 3.5 0.7 - - - -
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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