Contacts of the helix formed by residues 122 - 129 (chain B) in PDB entry 5M64
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 TYR 122 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LYS* 3.5 41.3 + - + -
121B VAL* 1.3 87.2 - - - +
123B PRO* 1.3 69.9 - - + +
124B SER* 4.3 8.1 - - - +
125B GLU* 3.4 19.0 + - + +
126B SER* 3.0 24.6 + - - -
133B TYR* 4.1 4.4 - - - -
171B HIS* 5.7 3.4 - - + -
175B MET* 5.8 1.3 - - + -
183B HIS* 3.3 43.1 + + + +
184B LYS* 4.6 9.4 - - - +
33L GLU* 3.3 38.2 + - + -
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Residues in contact with PRO 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL 4.7 0.7 - - - +
122B TYR* 1.3 88.5 - - + +
124B SER* 1.3 58.1 + - - +
126B SER* 2.9 23.1 + - - -
127B ARG* 3.1 16.7 + - - -
133B TYR* 3.8 24.0 - - + +
165B LEU* 3.6 27.4 - - + -
171B HIS* 6.4 0.2 - - - +
172B LEU* 3.6 31.2 - - + -
183B HIS* 6.0 2.9 - - + +
185B GLU* 3.3 21.3 - - + +
195B ILE* 5.1 3.6 - - + +
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Residues in contact with SER 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TYR* 3.3 2.9 - - - -
123B PRO* 1.3 79.0 - - - +
125B GLU* 1.3 61.4 + - - +
127B ARG* 3.4 15.7 + - - +
128B GLN* 3.2 27.4 + - - +
183B HIS 3.9 9.6 - - - -
184B LYS* 3.5 38.2 + - - +
185B GLU* 3.3 18.8 + - - -
735B HIS* 3.8 16.1 + - - +
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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
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119B ARG* 5.5 6.4 + - - -
121B VAL* 4.8 9.0 - - - +
122B TYR* 3.4 25.8 + - + +
123B PRO 3.2 0.6 - - - -
124B SER* 1.3 76.7 - - - +
126B SER* 1.3 63.3 + - - +
128B GLN* 3.8 6.5 - - - -
129B ARG* 3.0 43.2 + - - +
184B LYS* 5.3 5.9 - - - +
32L ALA* 5.7 1.1 - - + -
53L HIS* 3.4 35.9 - - + +
54L ARG* 5.4 4.0 + - - +
55L ILE* 3.5 20.0 + - + +
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Residues in contact with SER 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 6.4 0.9 - - - -
122B TYR 3.0 13.6 + - - -
123B PRO* 2.9 16.6 + - - -
125B GLU* 1.3 80.8 - - - +
127B ARG* 1.3 61.8 + - - +
129B ARG* 3.3 10.5 + - - +
131B THR* 3.2 26.3 + - - +
132B SER 3.4 6.2 + - - -
133B TYR* 3.3 38.0 + - - -
195B ILE* 3.4 6.9 - - - +
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Residues in contact with ARG 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 PRO* 3.1 25.6 + - - -
124B SER* 3.4 22.1 + - - +
126B SER* 1.3 76.9 + - - +
128B GLN* 1.3 63.1 + - - +
129B ARG 3.2 0.7 - - - -
130B LEU* 3.2 14.9 + - - +
131B THR 4.3 7.0 - - - -
184B LYS 4.4 7.1 + - - -
185B GLU* 4.6 11.7 + - - +
193B TYR* 4.3 11.3 + - - -
195B ILE* 4.4 23.6 - - + +
198B GLY* 3.9 20.0 - - - +
732B ALA* 4.1 11.7 - - - +
735B HIS 3.1 27.5 + - - +
736B ARG* 3.6 33.9 - - + +
737B SER* 3.5 26.1 - - - +
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Residues in contact with GLN 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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124B SER* 3.2 24.9 + - - +
125B GLU* 3.7 8.7 - - - +
126B SER 3.3 0.2 - - - -
127B ARG* 1.3 78.4 - - + +
129B ARG* 1.3 56.1 + - - +
130B LEU* 3.2 7.2 - - - +
734B CYS 4.1 5.5 + - - -
735B HIS* 3.2 43.6 - - + +
736B ARG 3.3 6.3 + - - +
737B SER* 3.0 22.7 + - - -
886B ASN* 4.0 25.7 + - - +
888B ILE* 3.3 21.7 - - - +
55L ILE* 3.8 21.1 - - + +
57L LEU* 6.0 1.3 - - - +
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Residues in contact with ARG 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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109B SER* 5.1 7.9 + - - -
119B ARG* 5.7 3.0 - - - +
121B VAL* 6.3 0.4 - - - +
125B GLU* 3.0 34.0 + - - +
126B SER* 3.5 7.4 - - - +
127B ARG 3.2 0.6 - - - -
128B GLN* 1.3 74.7 - - - +
130B LEU* 1.3 71.1 + - - +
131B THR* 3.3 24.4 + - + +
888B ILE* 3.3 22.7 - - + +
889B GLY 3.6 10.9 + - - +
890B ASP* 3.4 20.0 + - - +
891B GLU* 3.2 41.2 - - - +
54L ARG* 5.6 2.2 - - - +
55L ILE* 3.7 15.3 - - + -
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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