Contacts of the helix formed by residues 118 - 129 (chain A) in PDB entry 3OMA
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 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLY* 3.3 28.0 - - - -
33A TYR* 3.7 5.6 - - - -
34A LEU* 4.1 8.5 - - - -
113A PRO 2.8 9.9 + - - -
114A ALA 3.2 9.9 + - - -
116A PHE 3.3 1.0 - - - -
117A GLY* 1.3 73.2 - - - +
119A PHE* 1.3 62.4 + - - +
120A GLY 3.3 0.7 - - - -
122A TYR* 3.0 27.4 + - - +
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Residues in contact with PHE 119 (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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34A LEU* 3.9 29.4 - - + -
114A ALA 3.1 14.7 + - - -
115A LEU* 3.4 13.4 + - + +
118A GLY* 1.3 69.2 - - - -
120A GLY* 1.3 60.0 + - - +
122A TYR* 5.5 0.4 - - + -
123A PHE* 2.8 44.3 + + - +
228A PHE* 3.4 18.9 - - + -
297A ILE* 3.8 15.7 - - + -
432A ILE* 3.9 23.6 - - + -
435A GLY* 3.6 23.6 - - - -
436A ILE* 3.6 17.7 - - + -
439A TRP* 3.5 30.1 - + + -
443A MET* 3.9 15.5 - - + -
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Residues in contact with GLY 120 (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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115A LEU 2.9 11.1 + - - -
116A PHE 3.1 12.2 + - - -
119A PHE* 1.3 75.5 - - - +
121A ASN* 1.3 61.0 + - - +
124A MET* 3.1 29.2 + - - +
125A PRO* 3.6 0.9 - - - +
133A MET* 4.0 1.0 - - - +
208A MET* 3.8 8.1 - - - -
228A PHE* 3.7 3.3 - - - -
232A ILE* 3.7 25.6 - - - -
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Residues in contact with ASN 121 (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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26A HIS* 2.8 42.0 + - - +
29A ILE* 4.0 1.3 - - - +
30A GLY* 3.9 4.7 - - - +
33A TYR* 3.7 13.3 - - - -
116A PHE 3.3 4.8 + - - -
117A GLY* 2.8 36.0 + - - +
118A GLY 3.4 1.4 + - - -
120A GLY* 1.3 73.6 - - - +
122A TYR* 1.3 60.0 + - - +
125A PRO* 3.4 5.7 - - - +
133A MET* 3.3 15.9 - - - +
139A ASN* 2.9 40.1 + - - +
142A SER* 5.1 0.6 + - - -
204A GLY* 6.0 2.4 - - - -
207A ASN* 5.7 0.9 - - - +
208A MET* 3.7 10.3 - - - +
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Residues in contact with TYR 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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7A DMU 4.9 4.2 + - - -
26A HIS* 3.2 30.1 + - - -
27A LYS* 3.3 47.5 - - + +
30A GLY* 4.2 3.3 - - - -
31A VAL* 4.0 20.0 - - + -
34A LEU* 6.4 0.4 - - + -
118A GLY 3.0 17.4 + - - +
119A PHE* 4.5 0.4 - - - -
121A ASN* 1.3 75.9 - - - +
123A PHE* 1.3 97.9 + + + +
126A LEU* 3.5 23.5 - - + +
442A LYS* 5.1 0.7 - - + -
443A MET* 3.6 32.3 + - + -
545A PRO* 4.6 1.2 - - - +
546A PRO* 3.3 27.4 - - + +
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Residues in contact with PHE 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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119A PHE* 2.8 32.6 + + - +
122A TYR* 1.3 106.3 - + + +
124A MET* 1.3 57.3 + - - +
125A PRO 3.4 1.6 - - - -
126A LEU* 3.2 11.2 + - + +
127A HIS* 2.8 41.5 + - + -
228A PHE* 3.9 11.4 - - + -
439A TRP* 3.2 71.1 - + + -
442A LYS* 4.1 7.9 - - + -
443A MET* 3.8 15.5 - - + -
539A GLU* 3.9 20.6 - - + -
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Residues in contact with MET 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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119A PHE 3.9 0.8 + - - -
120A GLY* 3.1 21.8 + - - +
123A PHE* 1.3 77.0 - - - +
125A PRO* 1.3 67.0 - - + +
127A HIS* 3.2 7.5 + - - +
128A ILE* 3.2 40.1 + - - +
133A MET* 3.9 15.0 - - + -
208A MET* 3.4 50.7 - - + +
211A THR* 4.1 6.1 - - + -
212A PHE* 4.4 10.5 - - + -
228A PHE* 4.2 5.5 - - + -
229A ALA* 4.0 25.8 - - + +
232A ILE* 4.2 17.0 - - + -
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Residues in contact with PRO 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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26A HIS* 3.3 33.4 - - + +
120A GLY 3.6 2.2 - - - +
121A ASN 3.4 14.1 - - - +
123A PHE 3.6 1.8 - - - -
124A MET* 1.3 94.6 - - + +
126A LEU* 1.3 61.6 + - - +
128A ILE* 3.2 9.7 + - + +
129A GLY 3.0 4.0 + - - -
130A ALA* 2.8 47.2 + - + +
132A ASP 4.7 4.5 - - - -
133A MET* 3.4 27.6 - - + -
211A THR* 4.9 0.7 - - + -
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Residues in contact with LEU 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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26A HIS* 3.9 14.6 - - + +
27A LYS* 4.8 4.3 - - + -
122A TYR* 3.5 44.2 - - + +
123A PHE* 3.2 12.2 + - + +
125A PRO* 1.3 78.8 - - - +
127A HIS* 1.3 62.8 + - + +
129A GLY 3.4 6.4 + - - -
130A ALA 5.1 0.2 - - - +
538A LEU* 3.3 22.6 - - - +
539A GLU* 3.9 31.2 - - + -
542A LEU* 3.9 16.2 - - + -
546A PRO* 4.3 11.0 - - + -
550A THR* 3.9 22.0 - - + +
551A PHE* 3.7 11.0 - - + -
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Residues in contact with HIS 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 PHE* 2.8 23.2 + - + +
124A MET 3.2 5.1 + - - +
126A LEU* 1.3 73.4 - - - +
128A ILE* 1.3 58.5 + - - +
129A GLY 3.4 0.4 - - - -
220A MET* 3.5 12.5 - - - +
226A PRO* 3.5 32.2 - - + +
228A PHE* 3.5 33.4 - + + +
229A ALA* 4.2 12.0 + - + +
300A HIS* 3.3 29.2 - + - -
439A TRP* 3.9 11.4 - + - -
537A THR* 3.8 7.8 + - - -
538A LEU* 4.2 8.0 + - - +
539A GLU* 2.9 42.7 + - + -
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Residues in contact with ILE 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* 3.2 36.7 + - - +
125A PRO* 3.5 6.7 - - + +
127A HIS* 1.3 79.9 - - - +
129A GLY* 1.3 56.9 + - - +
130A ALA* 3.5 18.6 + - + -
211A THR* 3.7 24.5 - - + +
212A PHE* 3.9 11.9 - - + -
216A ARG* 3.5 23.7 - - + +
217A ALA* 2.9 26.5 + - - +
220A MET* 3.9 13.5 - - + +
225A VAL* 4.2 14.8 - - + -
229A ALA* 3.9 21.1 - - + -
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Residues in contact with GLY 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 PRO 3.0 4.8 + - - -
126A LEU 3.4 4.4 + - - -
127A HIS 3.4 0.6 - - - -
128A ILE* 1.3 79.0 - - - +
130A ALA* 1.3 61.8 + - - +
131A PRO* 3.9 3.1 - - - +
215A MET 4.3 1.6 - - - +
217A ALA* 4.0 18.0 + - - +
538A LEU* 3.7 15.3 - - - +
551A PHE* 3.7 32.9 - - - +
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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