Contacts of the strand formed by residues 125 - 132 (chain A) in PDB entry 3N4E
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 ARG 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A ARG* 3.7 15.7 - - - +
124A THR* 1.3 87.3 - - - +
126A LEU* 1.3 61.4 + - - +
127A PRO* 4.0 2.6 - - - +
343A VAL* 3.5 33.5 + - - +
344A ASP* 4.4 13.5 + - - +
346A HIS* 3.7 47.5 + - + +
347A PHE 3.3 4.7 - - - -
348A ALA* 3.8 25.7 - - + +
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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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123A ARG* 3.9 22.0 - - + +
124A THR* 3.8 17.5 - - - +
125A ARG* 1.3 77.7 - - - +
127A PRO* 1.3 70.6 - - + +
310A ILE* 3.9 27.4 - - + +
313A LEU* 3.9 23.6 - - + +
314A SER* 4.0 9.9 - - - +
319A MSE 4.5 6.3 - - + -
323A VAL* 3.9 21.8 - - + -
346A HIS* 3.2 2.6 - - - -
347A PHE* 2.7 50.2 + - + +
349A LEU* 4.3 11.4 - - + -
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Residues in contact with PRO 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 ARG* 5.5 0.9 - - - -
125A ARG 4.0 3.4 - - - +
126A LEU* 1.3 87.3 - - - +
128A CYS* 1.3 59.9 - - - +
157A ALA* 3.9 22.2 - - + -
319A MSE 3.7 26.2 - - + -
322A PRO* 3.4 9.9 - - + +
323A VAL* 2.9 24.9 + - - +
345A GLY 3.4 9.4 - - - +
346A HIS* 3.3 23.3 - - + +
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Residues in contact with CYS 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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127A PRO* 1.3 71.9 - - - +
129A TYR* 1.3 59.8 + - - +
154A GLU* 4.1 4.9 - - - -
156A PRO* 4.0 18.4 - - - -
157A ALA* 2.8 25.3 + - - +
322A PRO* 3.4 11.4 - - - +
323A VAL 3.2 6.3 - - - +
325A LEU* 4.3 13.5 - - + -
342A PRO* 4.0 21.3 - - + -
345A GLY 3.0 21.0 + - - +
347A PHE* 3.4 33.0 - - + -
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Residues in contact with TYR 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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128A CYS* 1.3 76.7 - - - +
130A SER* 1.3 65.7 + - - +
131A SER* 3.4 4.1 + - - -
156A PRO* 3.8 1.8 - - - -
158A ALA* 3.3 28.5 - - + +
160A LYS* 2.6 62.3 + - + +
221A TRP* 4.0 19.1 - + - -
223A GLU* 4.3 1.0 + - - -
269A GLN* 4.7 5.5 + - - -
296A VAL* 4.8 10.6 - - + +
297A PRO 5.1 2.6 + - - -
322A PRO* 3.5 35.0 - - + -
323A VAL 2.8 13.4 + - - -
324A GLU* 3.3 34.7 + - + +
325A LEU* 2.9 30.7 + - - +
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Residues in contact with SER 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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129A TYR* 1.3 71.0 - - - +
131A SER* 1.3 59.6 + - - +
132A ILE* 3.6 22.0 + - - +
150A ARG* 4.2 8.3 + - - -
151A VAL 5.2 0.7 - - - -
154A GLU* 2.7 28.1 + - - +
156A PRO* 3.1 27.8 - - - +
158A ALA 3.2 8.0 + - - -
159A VAL* 3.7 4.3 - - - -
160A LYS 2.9 28.8 + - - +
325A LEU 3.8 4.0 - - - -
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Residues in contact with SER 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 TYR* 3.4 8.0 + - - -
130A SER* 1.3 69.8 - - - +
132A ILE* 1.3 53.3 + - - +
150A ARG* 2.8 21.6 + - - +
160A LYS* 3.5 8.5 - - - -
162A ARG* 3.0 35.5 + - - -
324A GLU* 2.7 39.8 + - - -
325A LEU 2.8 18.2 + - - -
326A ALA* 3.9 2.0 - - - -
327A ASP* 3.3 8.3 + - - +
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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 SER* 3.7 18.6 - - - +
131A SER* 1.3 73.9 - - - +
133A GLY* 1.3 55.2 + - - +
135A ASN* 2.9 12.1 + - - +
138A ARG* 4.3 9.0 - - - +
146A GLU* 3.7 31.2 - - + +
147A VAL* 3.8 32.3 - - + +
150A ARG* 3.8 21.1 - - + +
151A VAL* 5.4 0.2 - - + -
159A VAL* 3.8 26.5 - - + -
160A LYS 2.9 11.7 + - - +
161A ILE* 4.6 3.1 - - + -
162A ARG* 2.7 32.3 + - - +
327A ASP* 3.7 5.4 - - - +
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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