Contacts of the strand formed by residues 137 - 142 (chain A) in PDB entry 2EYR
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 SER 137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A GLN* 3.2 27.2 + - - +
130A ASP* 3.3 11.2 + - - -
135A ASP 4.0 0.6 + - - -
136A LYS* 1.3 74.3 - - - +
138A VAL* 1.3 62.2 + - - +
139A CYS* 5.1 0.7 - - - -
181A TRP* 3.2 22.7 - - - -
182A SER 3.0 11.1 + - - -
184A LYS 5.8 2.0 - - - -
187A PHE* 3.3 32.5 + - - -
188A ALA* 5.9 0.2 - - - -
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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
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127A GLN* 3.6 8.0 - - - +
128A LEU* 2.9 44.5 + - + -
130A ASP* 3.9 5.1 + - - -
136A LYS* 4.8 0.4 - - + -
137A SER* 1.3 77.5 + - - +
139A CYS* 1.3 68.0 + - - +
179A VAL* 3.8 23.8 - - + -
180A ALA 3.4 2.0 - - - -
181A TRP* 3.9 5.8 - - + -
131B PHE* 3.7 31.4 - - + -
147B VAL* 4.0 14.8 - - + -
149B LEU* 3.6 30.3 - - + -
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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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125A VAL* 4.4 1.1 - - + -
126A TYR 3.2 4.9 - - - +
137A SER* 5.1 0.9 - - - -
138A VAL* 1.3 78.0 - - - +
140A LEU* 1.3 61.0 + - - +
141A PHE 4.1 0.2 - - - -
178A ALA 3.8 1.0 - - - +
179A VAL* 3.7 4.2 - - - -
180A ALA 2.8 37.3 + - - +
187A PHE* 3.5 27.4 - - - -
189A CYS* 2.0 56.8 - - + -
192A ALA* 3.9 3.1 - - + -
193A PHE* 4.0 18.1 - - + -
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Residues in contact with LEU 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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124A ALA 3.3 2.6 - - - +
125A VAL* 3.2 5.8 - - - -
126A TYR* 2.7 44.4 + - + +
128A LEU* 3.7 24.6 - - + +
139A CYS* 1.3 72.8 - - - +
141A PHE* 1.3 58.3 + - - +
142A THR* 3.7 22.8 + - + +
177A SER* 3.7 27.6 - - - +
178A ALA 3.7 8.1 - - - +
179A VAL* 4.3 15.7 - - + -
137B GLU* 4.5 4.0 - - - +
145B THR* 3.8 32.8 - - + +
147B VAL* 4.4 10.3 - - + -
196B ARG* 4.5 4.0 - - + -
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Residues in contact with PHE 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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123A PRO* 4.5 6.3 - - + -
124A ALA 3.4 12.3 - - - -
125A VAL* 3.6 12.6 - - + -
140A LEU* 1.3 72.7 - - - +
142A THR* 1.3 57.7 + - - +
144A PHE* 3.4 40.6 - + - -
148A THR* 3.8 16.2 - - + -
150A VAL* 4.4 11.2 - - + -
177A SER* 3.0 4.0 - - - -
178A ALA* 2.7 37.4 + - + +
193A PHE* 3.5 40.8 - + + -
196A SER* 5.6 2.2 - - - -
198A ILE* 3.6 29.6 - - + -
199A PRO* 4.0 9.2 - - + -
202A THR* 3.9 23.6 - - + -
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Residues in contact with THR 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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123A PRO* 3.3 1.0 - - - +
124A ALA* 2.9 33.1 + - + +
126A TYR* 3.5 37.2 - - + -
140A LEU* 4.0 13.9 - - + +
141A PHE* 1.3 76.0 - - - +
143A ASP* 1.3 91.0 + - + +
144A PHE* 3.2 7.8 + - - -
175A SER* 4.6 1.4 + - - -
176A ASN 3.0 13.7 + - - -
177A SER* 3.6 10.2 - - - -
145B THR* 5.4 0.3 + - - -
198B ARG* 4.1 11.5 + - - +
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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