Contacts of the strand formed by residues 321 - 328 (chain A) in PDB entry 4C48
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 321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A VAL* 3.8 25.1 - - + -
143A ILE 3.3 23.1 - - - +
144A ASN* 4.2 1.6 - - - +
149A MET* 4.8 11.2 - - - -
154A ILE* 4.2 13.0 - - + -
157A TYR* 3.6 40.8 - - + -
162A MET* 5.5 0.4 - - - -
317A PHE* 3.5 31.1 - - + +
318A PRO* 3.5 28.9 + - + +
319A SER 3.3 2.6 - - - +
320A GLY* 1.3 77.2 - - - +
322A LYS* 1.3 62.8 + - - +
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Residues in contact with LYS 322 (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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142A VAL* 3.4 3.0 - - - -
143A ILE* 2.9 42.9 + - + +
145A THR* 4.1 26.9 - - + -
317A PHE* 5.1 0.4 - - - -
321A LEU* 1.3 76.8 - - - +
323A ILE* 1.3 77.2 + - - +
324A VAL* 6.3 0.4 - - + -
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Residues in contact with ILE 323 (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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140A VAL* 3.6 22.9 - - + -
141A GLY 3.5 3.8 - - - -
142A VAL* 3.9 8.5 - - + -
162A MET* 3.6 26.7 - - + -
310A LEU* 3.5 28.9 - - + +
314A GLU* 6.2 0.9 - - + -
317A PHE* 3.7 24.9 - - + -
322A LYS* 1.3 88.4 - - - +
324A VAL* 1.3 68.3 + - - +
325A TYR* 3.8 30.1 - - + +
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Residues in contact with VAL 324 (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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140A VAL* 3.6 3.3 - - - +
141A GLY* 2.8 48.7 + - - +
142A VAL 4.5 1.3 - - - +
143A ILE* 4.5 12.3 - - + -
281A PHE* 3.3 50.7 - - + -
322A LYS* 5.1 0.7 - - + +
323A ILE* 1.3 81.7 - - - +
325A TYR* 1.3 72.7 + - + +
326A PRO* 3.0 4.5 - - + +
608A SER* 5.8 0.2 - - - +
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Residues in contact with TYR 325 (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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138A MET* 4.2 12.1 - - + -
139A VAL 4.2 4.9 - - - +
140A VAL* 3.5 28.3 - - + -
307A ARG* 3.9 34.6 + - - -
310A LEU* 4.5 6.7 - - + +
323A ILE* 3.8 23.1 - - + +
324A VAL* 1.3 87.8 - - + +
326A PRO* 1.3 64.9 - - - +
327A TYR 3.2 5.4 + - - -
328A ASP* 4.7 16.6 - - + +
630A SER* 5.2 2.8 + - - -
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Residues in contact with PRO 326 (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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139A VAL* 3.4 22.9 - - + +
141A GLY 3.9 4.7 - - - +
281A PHE* 4.0 8.7 - - + -
324A VAL* 3.0 20.1 - - + +
325A TYR* 1.3 82.9 - - - +
327A TYR* 1.3 61.6 + - + +
608A SER* 3.9 20.6 - - - +
610A PHE* 3.9 41.5 - - + +
628A PHE* 4.9 1.9 - - + +
629A VAL 4.3 1.4 - - - -
630A SER* 3.2 30.8 + - - -
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Residues in contact with TYR 327 (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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135A SER* 6.0 1.2 - - - -
136A PHE* 3.4 38.2 + + + +
137A LEU 4.6 2.0 - - - -
138A MET* 3.2 7.3 - - - +
139A VAL* 3.0 51.2 + - + +
325A TYR* 3.2 3.1 + - - +
326A PRO* 1.3 84.6 - - + +
328A ASP* 1.3 62.0 + - - +
329A THR* 4.9 4.8 + - - -
571A VAL* 4.3 27.8 - - + -
572A PHE 4.6 5.6 - - - -
573A MET* 3.7 26.6 - - + +
628A PHE* 4.2 24.2 - + + -
629A VAL 5.0 0.9 - - - -
668A LEU* 3.1 30.5 - - + +
672A VAL* 5.7 2.1 - - - +
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Residues in contact with ASP 328 (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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137A LEU* 4.4 0.7 - - - +
138A MET* 3.6 34.2 - - + +
325A TYR* 4.7 16.9 - - + +
327A TYR* 1.3 77.1 - - - +
329A THR* 1.3 67.5 + - - +
330A THR* 3.1 28.1 + - - +
331A PRO* 3.4 20.7 - - + +
332A PHE* 5.0 2.1 + - - +
569A GLN 5.3 2.3 - - - +
571A VAL* 4.2 18.9 - - - +
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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