Contacts of the strand formed by residues 138 - 144 (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 MET 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A PHE* 3.8 2.3 - - - +
137A LEU* 1.3 93.3 - - + +
139A VAL* 1.3 75.3 + - - +
140A VAL* 3.7 24.5 - - + -
291A ILE* 3.3 38.1 + - + +
303A ALA* 4.5 9.6 - - + +
306A ILE* 4.1 25.4 - - + -
307A ARG* 6.4 2.2 - - + -
325A TYR* 4.2 13.0 - - + -
327A TYR* 3.2 19.1 - - - +
328A ASP* 3.6 27.1 - - + +
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Residues in contact with VAL 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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136A PHE* 4.4 7.0 - - + -
138A MET* 1.3 83.5 - - - +
140A VAL* 1.3 73.4 - - - +
178A PHE* 4.1 14.6 - - + -
289A LEU 3.3 9.0 - - - +
290A GLY* 3.7 16.2 - - - -
325A TYR* 4.2 2.3 - - - +
326A PRO* 3.4 29.7 - - + +
327A TYR* 3.0 28.7 + - + +
610A PHE* 4.3 9.4 - - + -
628A PHE* 3.6 30.5 - - + -
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Residues in contact with VAL 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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138A MET* 3.7 22.3 - - + +
139A VAL* 1.3 76.0 - - - +
141A GLY* 1.3 73.4 + - - +
142A VAL* 4.8 2.9 - - + +
162A MET* 5.7 0.9 - - + -
288A GLY* 3.1 1.7 - - - -
289A LEU* 2.7 43.0 + - + +
291A ILE* 5.5 4.3 - - + -
306A ILE* 5.7 2.7 - - + -
310A LEU* 4.3 21.5 - - + -
323A ILE* 3.6 18.4 - - + -
324A VAL 3.6 2.5 - - - -
325A TYR* 3.5 31.2 - - + -
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Residues in contact with GLY 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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140A VAL* 1.3 79.3 - - - +
142A VAL* 1.3 71.1 + - - +
286A ALA* 5.9 0.7 - - - -
287A SER 3.3 12.3 - - - -
288A GLY* 3.7 2.0 - - - -
323A ILE* 3.5 0.5 - - - -
324A VAL* 2.8 40.1 + - - -
326A PRO* 3.9 4.4 - - - +
610A PHE* 4.5 12.3 - - - -
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Residues in contact with VAL 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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140A VAL* 4.8 3.4 - - + +
141A GLY* 1.3 80.1 - - - +
143A ILE* 1.3 62.1 + - - +
154A ILE* 3.4 26.7 - - + +
158A VAL* 3.5 26.9 - - + -
162A MET* 4.1 14.8 - - + -
286A ALA* 3.4 16.2 - - - +
287A SER 2.9 15.9 + - - +
288A GLY* 5.7 0.7 - - - -
317A PHE* 5.5 0.2 - - + -
321A LEU* 3.8 20.6 - - + -
322A LYS 3.4 11.7 - - - +
323A ILE* 3.9 20.0 - - + -
324A VAL* 4.7 1.8 - - - -
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Residues in contact with ILE 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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142A VAL* 1.3 75.8 - - - +
144A ASN* 1.3 84.0 + - + +
145A THR* 3.9 3.9 + - + +
149A MET 5.9 1.1 - - - +
154A ILE* 4.6 5.4 - - + -
281A PHE* 4.7 12.3 - - + -
284A GLN* 3.0 41.1 - - + +
285A PRO* 2.9 33.7 - - + +
286A ALA* 4.7 4.7 - - + -
321A LEU* 3.3 7.7 - - - +
322A LYS* 2.9 44.2 + - + +
324A VAL* 4.5 14.6 - - + -
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Residues in contact with ASN 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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143A ILE* 1.3 95.5 - - + +
145A THR* 1.3 60.3 + - - +
146A ASP* 2.6 32.2 + - - +
147A GLY* 3.5 15.0 + - - +
148A THR* 2.5 29.0 + - - +
149A MET* 3.0 44.0 - - + +
154A ILE* 4.3 7.9 - - + +
284A GLN* 3.5 5.4 - - - +
319A SER 4.1 5.1 + - - -
320A GLY 2.8 22.0 - - - +
321A LEU* 4.2 3.4 - - + +
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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