Contacts of the helix formed by residues 125 - 137 (chain A) in PDB entry 4H3E
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 PRO 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A ALA 3.3 8.9 - - - +
124A MET* 1.3 84.3 - - + +
126A LYS* 1.3 65.8 + - - +
127A SER* 3.2 7.2 - - - +
128A PHE* 3.1 6.3 + - + +
129A GLU* 3.0 20.3 + - - +
221A TRP 3.6 19.5 - - - +
222A GLU* 4.4 13.7 - - + +
225A ALA* 3.6 23.8 - - + -
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Residues in contact with LYS 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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124A MET 3.6 2.3 + - - -
125A PRO* 1.3 72.0 - - - +
127A SER* 1.3 65.4 + - - +
129A GLU* 3.4 11.7 + - - +
130A SER* 3.0 24.9 + - - -
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Residues in contact with SER 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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125A PRO* 3.2 5.5 - - - +
126A LYS* 1.3 82.0 - - - +
128A PHE* 1.3 61.1 + - - +
130A SER* 3.5 7.3 + - - -
131A ALA* 3.4 18.5 + - - +
228A HIS* 5.5 2.1 - - - -
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Residues in contact with PHE 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 MET* 4.0 17.7 - - + -
125A PRO* 3.1 10.0 + - + +
127A SER* 1.3 75.6 - - - +
129A GLU* 1.3 68.2 + - - +
131A ALA* 3.0 15.2 + - + +
132A VAL* 3.1 36.4 + - + +
161A LEU* 4.0 16.4 - - + -
171A LEU* 4.7 5.2 - - + -
190A VAL* 4.5 5.6 - - + -
221A TRP* 3.8 27.6 - + - -
224A VAL* 3.5 20.2 - - + -
225A ALA* 3.7 28.7 - - + -
228A HIS* 3.7 45.3 - + + -
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Residues in contact with GLU 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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124A MET* 3.7 27.5 - - + +
125A PRO 3.0 16.3 + - - +
126A LYS* 3.4 11.8 + - - +
128A PHE* 1.3 78.3 - - - +
130A SER* 1.3 56.8 + - - +
132A VAL* 3.4 3.6 + - - +
133A THR* 2.8 37.6 + - - +
139A VAL* 3.8 22.6 - - + +
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Residues in contact with SER 130 (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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126A LYS 3.0 16.8 + - - -
127A SER* 3.6 8.1 - - - -
129A GLU* 1.3 78.7 + - - +
131A ALA* 1.3 55.8 + - - +
133A THR* 3.8 6.1 - - - -
134A ALA* 2.9 30.3 + - - +
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Residues in contact with ALA 131 (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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127A SER 3.4 9.1 + - - +
128A PHE* 3.0 10.1 + - + +
130A SER* 1.3 76.7 - - - +
132A VAL* 1.3 62.9 + - - +
134A ALA* 3.9 5.1 - - - +
135A GLN* 3.2 25.1 + - - +
171A LEU* 3.7 8.4 - - + +
228A HIS* 3.6 32.8 - - + +
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Residues in contact with VAL 132 (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 MET* 4.7 6.3 - - + -
128A PHE* 3.1 47.2 + - + +
129A GLU* 3.7 7.9 - - - +
131A ALA* 1.3 72.8 - - - +
133A THR* 1.3 61.2 + - - +
136A PHE* 2.8 35.4 + - + +
138A SER 4.3 0.4 - - - +
139A VAL* 4.1 19.7 - - + -
142A PHE* 3.5 38.1 - - + -
161A LEU* 5.0 5.6 - - + -
171A LEU* 4.3 10.1 - - + -
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Residues in contact with THR 133 (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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129A GLU* 2.8 32.9 + - - +
130A SER* 3.8 7.4 - - - -
132A VAL* 1.3 74.8 - - - +
134A ALA* 1.3 59.6 + - - +
137A GLY* 2.8 51.6 + - - +
138A SER* 4.2 6.1 - - - +
139A VAL* 4.2 10.4 + - - +
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Residues in contact with ALA 134 (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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130A SER* 2.9 19.0 + - - +
131A ALA* 3.9 7.0 - - - +
133A THR* 1.3 79.0 - - - +
135A GLN* 1.3 59.2 + - - +
137A GLY* 4.4 1.6 + - - -
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Residues in contact with GLN 135 (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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131A ALA 3.2 15.9 + - - +
133A THR 3.2 0.6 - - - -
134A ALA* 1.3 81.8 - - - +
136A PHE* 1.3 89.3 + - + +
137A GLY 3.6 0.2 - - - -
170A GLN* 3.6 15.3 - - - +
171A LEU* 3.3 37.9 + - + +
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Residues in contact with PHE 136 (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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132A VAL* 2.8 25.1 + - + +
135A GLN* 1.3 96.6 - - + +
137A GLY* 1.3 58.0 + - - +
138A SER 3.2 7.6 + - - +
141A GLN* 3.4 22.9 + - - +
142A PHE* 3.7 47.3 - + + +
145A ALA* 5.2 3.8 - - + -
161A LEU* 3.9 18.4 - - + -
171A LEU* 3.9 26.2 - - + -
172A VAL 4.6 0.2 - - - -
173A ILE* 4.0 24.7 - - + -
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Residues in contact with GLY 137 (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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133A THR* 2.8 31.0 + - - +
134A ALA 4.4 1.5 + - - -
135A GLN 3.6 1.8 - - - -
136A PHE* 1.3 75.4 - - - +
138A SER* 1.3 60.8 + - - +
141A GLN* 3.4 11.1 - - - +
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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