Contacts of the helix formed by residues 125 - 133 (chain A) in PDB entry 4GJC
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 PHE 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A SER* 2.6 23.7 + - - -
124A GLY* 1.3 76.3 - - - -
126A ILE* 1.3 58.5 + - - +
127A GLU* 3.2 14.8 - - - +
128A GLN* 2.9 24.0 + - - +
135A PRO* 4.0 0.9 - - - -
184A LEU* 3.6 22.9 - - + -
187A THR* 3.7 9.0 - - - -
188A GLY* 3.3 32.3 - - - +
189A VAL 3.4 15.0 - - - -
190A TRP* 3.4 39.5 - + - -
315A ARG* 3.3 41.3 - - - +
318A ASN* 3.7 15.9 - - - -
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Residues in contact with ILE 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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125A PHE* 1.3 70.5 - - - +
127A GLU* 1.4 72.0 + - + +
129A ALA* 3.0 26.4 + - - +
132A ARG* 4.0 26.4 - - + +
133A VAL 3.7 12.8 - - - +
134A THR* 3.9 28.7 - - + +
135A PRO* 3.6 18.7 - - + +
138A ASP* 4.3 12.2 + - - +
315A ARG* 5.7 1.5 - - - +
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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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125A PHE* 3.1 16.4 + - - +
126A ILE* 1.4 86.4 - - + +
128A GLN* 1.4 58.3 + - - +
129A ALA 4.9 1.0 - - - +
187A THR* 4.0 17.5 + - - +
188A GLY* 3.6 34.1 + - - +
189A VAL* 6.0 0.4 - - + -
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Residues in contact with GLN 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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33A THR 4.4 4.0 + - - +
34A GLY* 3.6 24.0 - - - +
35A SER* 5.1 2.0 - - - -
36A SER* 3.3 20.1 + - - +
37A ASN* 4.2 3.3 - - - +
124A GLY* 3.8 7.8 - - - -
125A PHE* 2.9 26.1 + - - +
127A GLU* 1.4 75.1 - - - +
129A ALA* 1.3 62.0 + - - +
130A ILE* 3.5 13.7 + - - +
188A GLY 2.8 25.4 + - - +
189A VAL* 3.6 31.5 - - + +
190A TRP 4.5 0.4 - - - +
213A LEU* 5.3 0.5 - - - +
295A THR* 5.2 6.6 + - - +
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Residues in contact with ALA 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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36A SER* 3.8 20.8 - - - +
37A ASN* 3.6 8.3 - - - +
125A PHE 3.6 2.2 + - - -
126A ILE* 3.0 19.4 + - + +
127A GLU 4.9 1.7 - - - +
128A GLN* 1.3 76.2 - - - +
130A ILE* 1.3 65.1 + - - +
131A GLY 3.6 0.3 + - - -
132A ARG* 3.2 15.1 + - - +
133A VAL* 3.3 31.9 - - - +
135A PRO* 4.6 0.2 - - + -
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Residues in contact with ILE 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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37A ASN* 3.0 26.1 + - - +
71A LEU* 4.2 19.1 - - + +
72A THR 3.5 23.1 - - - +
73A LEU* 3.7 28.3 - - + -
74A ARG* 6.0 1.1 - - - +
128A GLN 4.3 10.8 - - - +
129A ALA* 1.3 71.5 - - - +
131A GLY* 1.3 64.5 + - - +
133A VAL* 3.5 10.2 - - - +
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Residues in contact with GLY 131 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A THR* 6.3 2.5 - - - -
71A LEU* 6.0 2.7 - - - -
84A LEU* 5.3 6.1 - - - +
129A ALA 3.6 0.4 + - - -
130A ILE* 1.3 73.4 - - - +
132A ARG* 1.4 72.9 + - - +
133A VAL* 3.2 13.1 + - - +
1000A NAG 4.9 4.5 + - - -
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Residues in contact with ARG 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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126A ILE* 4.0 22.9 - - + +
129A ALA* 3.2 16.0 + - - +
130A ILE 3.2 3.0 - - - -
131A GLY* 1.4 80.5 + - - +
133A VAL* 1.3 62.5 - - - +
134A THR* 3.7 2.4 + - - -
1000A NAG 5.2 2.6 + - - -
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Residues in contact with VAL 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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36A SER 4.9 1.4 - - - +
37A ASN* 4.5 11.4 - - - +
84A LEU* 3.7 35.4 - - + -
99A GLN* 4.5 0.4 - - - +
100A MET* 3.5 44.4 - - + +
101A PHE* 5.5 0.2 - - - -
126A ILE* 3.7 2.0 - - - +
129A ALA* 3.3 21.2 - - + +
130A ILE 3.5 19.1 + - - +
131A GLY 3.8 6.7 - - - +
132A ARG* 1.3 76.2 - - - +
134A THR* 1.3 72.5 + - - +
135A PRO* 3.3 4.0 - - - +
1000A NAG 4.8 9.4 - - - +
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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