Contacts of the strand formed by residues 134 - 144 (chain A) in PDB entry 5MY4
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 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A GLN* 3.0 42.2 + - - +
130A LEU* 3.3 7.9 + - - -
132A SER* 3.5 2.0 - - - -
133A GLY* 1.3 80.3 - - - +
135A ALA* 1.3 61.2 + - - +
185A THR* 6.1 0.4 - - - -
186A LEU 3.6 8.5 - - - -
187A THR* 4.3 0.4 - - - -
188A LYS 3.9 3.4 - - - -
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Residues in contact with ALA 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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125A PRO* 3.8 11.9 - - + -
129A GLN* 3.5 2.4 - - - +
130A LEU* 3.6 15.3 - - + -
134A GLY* 1.3 75.7 - - - +
136A SER* 1.3 58.3 + - - +
137A VAL* 4.0 1.6 + - - +
184A LEU 3.6 2.3 - - - +
185A THR* 4.5 0.2 - - - -
186A LEU* 2.7 44.5 + - - +
187A THR 4.0 2.9 - - - +
191A TYR* 3.5 37.7 - - + -
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO 3.8 1.9 - - - +
125A PRO* 3.3 24.5 - - - +
129A GLN* 3.0 30.1 + - - +
135A ALA* 1.3 73.0 - - - +
137A VAL* 1.3 61.5 + - - +
138A VAL* 4.0 5.0 + - - +
183A THR* 4.1 8.4 - - - +
184A LEU 3.2 4.7 - - - -
185A THR* 2.8 23.1 + - - -
133B LEU* 5.8 0.7 - - - +
150B LEU* 3.7 20.5 - - - +
152B LYS* 3.8 8.0 - - - -
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Residues in contact with VAL 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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122A ILE* 4.2 2.5 - - + -
123A PHE 3.5 6.7 - - - +
125A PRO* 4.0 13.9 - - + -
135A ALA 4.8 0.9 - - - +
136A SER* 1.3 75.9 - - - +
138A VAL* 1.3 59.6 + - - +
153A TRP* 3.4 32.4 - - + -
183A THR* 3.4 1.6 - - - -
184A LEU* 2.6 51.6 + - + +
186A LEU* 4.8 3.6 - - + -
191A TYR* 4.5 7.6 - - + -
197A TYR* 4.3 19.7 - - + -
214A PHE* 3.4 35.2 - - + -
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Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 3.4 4.2 - - - +
123A PHE* 2.8 41.4 + - + +
136A SER 4.5 5.6 - - - +
137A VAL* 1.3 77.3 - - - +
139A CYS* 1.3 65.8 + - - +
140A PHE* 3.9 28.5 - - + -
153A TRP* 4.1 0.7 - - - -
181A SER* 4.5 2.2 - - - +
182A SER 3.6 2.7 - - - +
183A THR* 4.1 26.7 - - + +
133B LEU* 3.8 36.8 - - + -
150B LEU* 4.4 14.6 - - + -
187B SER* 5.2 2.5 - - - +
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Residues in contact with CYS 139 (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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120A VAL* 3.4 22.4 - - - -
121A SER 3.2 8.1 - - - +
122A ILE* 4.6 0.9 - - + -
138A VAL* 1.3 76.4 - - - +
140A PHE* 1.3 63.3 + - - +
141A LEU* 3.7 10.8 - - - +
153A TRP* 3.7 12.3 - - + -
181A SER* 3.6 1.9 - - - -
182A SER* 2.8 41.1 + - - +
199A CYS* 2.1 52.5 - - + -
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Residues in contact with PHE 140 (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 THR 3.3 2.0 - - - +
120A VAL* 3.1 8.5 - - - +
121A SER* 2.9 36.9 + - - +
123A PHE* 3.4 29.6 - + - -
138A VAL* 3.9 9.2 - - + -
139A CYS* 1.3 77.5 - - - +
141A LEU* 1.3 61.0 + - - +
142A ASN* 4.0 15.5 - - - +
180A MET 3.6 1.8 - - - -
181A SER* 4.1 4.7 - - - -
133B LEU* 3.7 23.3 - - + -
146B THR* 4.0 7.4 - - + -
147B LEU 3.8 9.9 - - - -
148B GLY* 4.0 4.7 - - - -
175B PHE* 3.4 31.0 - + - -
187B SER* 3.8 15.5 - - - -
188B SER 3.9 8.3 - - - -
189B SER* 3.5 26.0 - - - -
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Residues in contact with LEU 141 (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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118A PRO* 4.3 6.5 - - + -
119A THR 3.3 5.6 - - - -
120A VAL* 4.3 8.1 - - + -
139A CYS* 3.7 27.4 - - - +
140A PHE* 1.3 77.7 - - - +
142A ASN* 1.3 56.6 + - - +
144A PHE* 3.2 20.7 - - + -
149A ILE* 4.0 10.5 - - + -
151A VAL* 3.5 28.5 - - + -
180A MET* 2.7 67.5 + - + +
182A SER* 4.4 2.0 - - - -
201A ALA* 3.5 26.2 - - + -
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Residues in contact with ASN 142 (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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118A PRO* 3.5 0.9 - - - +
119A THR* 2.9 41.1 + - + +
140A PHE* 4.0 10.4 - - - +
141A LEU* 1.3 82.1 + - - +
143A ASN* 1.3 82.6 + - + +
144A PHE* 3.5 2.8 + - - -
179A SER* 3.3 7.0 + - - -
146B THR* 4.5 9.9 + - - +
173B HIS* 3.2 15.5 - - - +
175B PHE* 3.5 19.6 - - - -
189B SER* 3.1 28.9 + - - -
191B THR* 4.8 5.1 + - - -
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Residues in contact with ASN 143 (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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116A ALA* 3.8 11.1 - - - +
117A ALA 3.8 10.4 - - - +
119A THR* 5.5 3.4 - - - +
142A ASN* 1.3 77.6 - - - +
144A PHE* 1.3 60.1 + - - +
175A ASP* 3.5 17.2 + - - +
177A THR* 3.5 20.6 - - + +
178A TYR 2.9 12.6 + - - -
179A SER* 3.0 1.6 + - - -
173B HIS* 2.6 39.0 + - - -
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Residues in contact with PHE 144 (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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116A ALA* 3.2 13.5 - - - +
118A PRO* 3.6 32.8 - - + -
141A LEU* 3.2 33.0 - - + -
143A ASN* 1.3 75.2 - - - +
145A TYR* 1.3 62.8 + - - +
146A PRO 3.2 20.2 - - - -
147A LYS 3.5 22.4 - - - -
149A ILE* 3.6 24.2 - - + -
168A TRP* 4.8 3.6 - + - -
177A THR* 3.4 3.2 - - - -
178A TYR* 2.7 58.9 + - + +
179A SER* 3.9 3.4 - - - -
180A MET* 4.0 14.4 - - + -
203A HIS* 3.8 8.7 - + - +
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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