Contacts of the strand formed by residues 127 - 132 (chain A) in PDB entry 5G04
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 LEU 127 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A GLN* 3.9 22.2 - - - +
93A LEU* 4.1 3.1 - - - -
125A GLN* 3.2 8.1 + - - +
126A ALA* 1.3 75.9 - - - +
128A TRP* 1.3 54.0 - - - +
151A ILE 3.7 0.2 - - - -
152A CYS* 2.7 57.5 + - + +
180A VAL* 3.1 50.0 - - + +
182A PRO* 3.4 40.6 - - + -
187A LEU* 4.5 8.1 - - + -
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Residues in contact with TRP 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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75A GLN* 4.1 21.5 + - + -
76A LEU 4.5 1.3 - - - -
77A ARG* 3.3 65.6 - - + +
91A GLU* 4.1 11.9 - - + -
92A GLU 3.7 4.5 - - - -
93A LEU* 3.3 51.2 - - + +
102A TRP* 3.7 44.6 - + - -
127A LEU* 1.3 74.6 - - - +
129A CYS* 1.3 60.3 + - - +
149A LYS 5.8 0.7 - - - -
150A CYS 3.5 15.9 - - - +
151A ILE* 3.9 14.9 - - + +
152A CYS* 4.4 0.4 - - - -
182A PRO* 3.1 24.5 - - - +
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Residues in contact with CYS 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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77A ARG* 6.3 0.2 - - - -
128A TRP* 1.3 76.5 - - - +
130A ASP* 1.3 78.5 + - - +
131A PHE* 3.2 42.6 - - - -
149A LYS* 3.6 0.3 - - - +
150A CYS* 3.0 29.6 + - - +
152A CYS* 3.8 7.4 - - - -
182A PRO 4.0 13.5 - - - +
183A THR 4.6 0.2 - - - +
186A GLY 4.2 3.1 - - - +
187A LEU* 3.7 28.0 - - + -
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Residues in contact with ASP 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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77A ARG* 5.7 1.9 + - - -
129A CYS* 1.3 92.0 - - - +
131A PHE* 1.3 65.6 + - - +
132A ILE* 4.3 0.9 + - - +
147A VAL* 3.9 22.3 - - + +
148A GLU 3.2 6.3 - - - +
149A LYS* 3.2 40.0 + - - +
182A PRO 5.3 0.2 + - - -
183A THR 4.4 5.3 + - - +
184A LYS 5.6 0.2 - - - -
185A TYR 5.1 3.3 + - - -
186A GLY* 3.8 15.8 + - - +
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Residues in contact with PHE 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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129A CYS* 3.2 29.2 - - - -
130A ASP* 1.3 76.9 - - - +
132A ILE* 1.3 62.0 + - - +
133A ILE* 3.8 4.3 + - - +
146A GLU 3.9 0.3 - - - +
147A VAL* 3.3 22.7 - - - -
148A GLU* 3.2 17.0 + - + +
150A CYS* 3.8 31.9 - - + -
152A CYS* 4.4 0.2 - - - -
161A MET* 3.5 33.4 - - + -
186A GLY 4.9 1.6 - - - -
187A LEU* 4.3 10.8 - - + -
213A MET* 4.4 7.9 - - + -
214A LEU* 3.1 27.4 - - - +
215A HIS* 3.5 20.0 - + + +
216A PRO* 3.4 29.6 - - + -
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Residues in contact with ILE 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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130A ASP 5.7 1.1 - - - +
131A PHE* 1.3 73.0 - - - +
133A ILE* 1.3 67.1 + - - +
134A SER* 4.0 12.7 + - - +
146A GLU* 4.5 3.6 - - - +
147A VAL* 3.6 21.8 - - + -
185A TYR* 4.0 27.8 - - + +
214A LEU* 3.6 35.4 - - + +
273A ARG* 4.1 25.1 - - - +
454C LYS* 3.9 0.9 + - - -
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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