Contacts of the helix formed by residues 121 - 129 (chain A) in PDB entry 4MSP
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 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A PRO* 3.3 7.8 + - - -
120A ARG* 1.3 75.9 - - - +
122A HIS* 1.3 64.6 + - - +
123A GLU* 3.8 9.7 + - - +
124A SER* 2.8 40.0 + - - -
125A PHE 3.2 9.0 + - - -
185A PHE* 3.7 9.0 - - - -
203B PGO 4.2 6.8 - - - -
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Residues in contact with HIS 122 (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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121A SER* 1.3 72.1 - - - +
123A GLU* 1.3 64.0 + - + +
125A PHE* 3.1 11.1 + + - +
126A GLN* 3.0 64.7 + - - +
134A TRP* 3.5 25.8 - + - -
182A ALA* 6.3 1.6 - - + -
185A PHE* 6.1 0.4 - - - -
3B ILE* 3.3 48.2 - - + +
4B PRO* 5.6 4.0 - - + -
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Residues in contact with GLU 123 (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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121A SER* 4.0 8.7 - - - +
122A HIS* 1.3 80.6 - - + +
124A SER* 1.3 61.6 + - - +
126A GLN* 3.4 13.3 + - - +
127A GLU* 2.9 25.3 + - - +
74B LYS* 2.3 52.2 + - + +
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Residues in contact with SER 124 (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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121A SER* 2.8 26.9 + - - -
123A GLU* 1.3 77.0 - - - +
125A PHE* 1.3 62.7 + - - +
127A GLU* 3.3 13.7 + - - +
128A MET* 3.1 29.8 + - - +
144A TYR* 5.6 3.7 + - - -
185A PHE* 4.5 2.2 - - - -
203B PGO 2.7 42.0 + - - -
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Residues in contact with PHE 125 (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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121A SER 3.2 3.9 + - - +
122A HIS* 3.1 14.6 + + + +
124A SER* 1.3 78.7 - - - +
126A GLN* 1.3 59.7 + - + +
128A MET* 3.1 6.9 + - - +
129A ASP* 2.8 38.2 + - + +
134A TRP* 3.4 66.6 - + - -
135A LYS* 3.9 5.2 - - - -
136A LEU* 3.6 23.2 - - + +
180A ILE 3.7 6.7 - - - -
182A ALA* 3.6 23.8 - - + -
185A PHE* 3.4 46.6 - + + -
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Residues in contact with GLN 126 (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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122A HIS* 3.0 53.4 + - + +
123A GLU* 3.8 12.2 - - - +
125A PHE* 1.3 76.3 - - - +
127A GLU* 1.3 61.4 + - - +
129A ASP* 3.3 11.5 + - - +
134A TRP* 3.5 24.0 - - + -
22B LYS* 2.9 32.1 + - - +
75B GLY* 5.4 4.5 - - - -
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Residues in contact with GLU 127 (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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123A GLU 2.9 17.1 + - - +
124A SER* 3.6 13.4 + - - +
125A PHE 3.2 0.2 - - - -
126A GLN* 1.3 76.3 - - - +
128A MET* 1.3 60.5 + - - +
130A LEU* 3.8 7.6 - - - +
144A TYR* 3.5 13.4 + - + -
147A LYS* 2.8 34.3 + - - +
22B LYS* 3.5 25.2 + - - +
23B THR 4.1 15.0 - - - +
24B LYS* 3.1 43.6 + - - +
75B GLY* 4.8 5.7 - - - +
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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 SER* 3.1 18.6 + - - +
125A PHE 3.7 3.8 - - - +
127A GLU* 1.3 76.7 - - - +
129A ASP* 1.3 52.6 + - - +
130A LEU* 2.8 22.5 + - - +
136A LEU* 4.0 19.5 - - + -
140A GLU* 3.4 23.3 - - + +
141A VAL* 3.8 30.1 - - + -
144A TYR* 3.6 58.1 - - + -
185A PHE* 4.7 8.1 - - - -
204A 1PE 3.9 25.1 - - - +
203B PGO 4.9 7.0 - - - -
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Residues in contact with ASP 129 (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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125A PHE* 2.8 24.5 + - + +
126A GLN* 3.3 9.9 + - - +
128A MET* 1.3 72.2 - - - +
130A LEU* 1.3 60.6 + - - +
131A ASN* 3.2 5.7 - - - +
132A ASP* 3.2 15.5 + - - -
133A ASP* 3.3 1.0 - - - +
134A TRP* 2.8 33.5 + - - -
135A LYS 3.1 6.0 - - - +
136A LEU* 3.6 12.3 - - + +
140A GLU* 4.0 1.6 - - - -
201A CA 2.3 31.7 - - - -
22B LYS* 2.9 20.2 + - - +
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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