Contacts of the strand formed by residues 448 - 461 (chain X) in PDB entry 4HSC
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 ASN 448 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126X LYS* 3.0 36.3 + - - +
156X ILE* 3.5 2.5 - - - +
157X ASN* 3.2 4.9 - - - +
158X THR* 2.7 45.1 + - + +
160X PRO* 3.8 17.2 - - - +
261X SER 5.2 1.0 - - - +
264X GLU* 4.9 2.5 + - - +
265X ALA* 3.7 30.0 + - + +
268X ASN* 5.5 1.6 + - - +
446X VAL* 3.2 20.6 + - - +
447X ASN* 1.3 70.7 - - - +
449X ARG* 1.3 60.0 + - - +
450X THR* 4.2 0.4 - - + -
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Residues in contact with ARG 449 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121X LEU* 5.4 2.6 - - - +
125X ALA* 3.3 27.5 - - - +
126X LYS 3.0 7.9 + - - +
127X ASN* 2.5 37.2 + - - +
128X GLY 2.7 31.0 + - - -
155X ASN* 5.4 3.6 - - - +
156X ILE 3.3 3.6 - - - +
157X ASN* 3.1 38.6 - - + +
447X ASN* 3.0 28.2 + - - +
448X ASN* 1.3 72.0 - - - +
450X THR* 1.3 54.9 + - - +
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Residues in contact with THR 450 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128X GLY* 3.7 9.6 - - - -
129X GLU 3.0 15.4 + - - -
154X LYS 4.1 0.2 - - - +
155X ASN* 3.7 5.8 + - - +
156X ILE* 2.9 44.6 + - + +
261X SER* 3.0 42.5 + - - +
262X GLN* 4.1 13.2 - - + -
265X ALA* 4.8 2.5 - - + -
448X ASN* 4.2 0.4 - - + -
449X ARG* 1.3 75.7 - - - +
451X GLU* 1.3 76.5 + - - +
452X TYR* 4.5 1.0 - - + -
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Residues in contact with GLU 451 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129X GLU* 3.1 27.8 + - - +
130X THR* 3.5 12.7 - - - +
131X ILE* 2.9 31.5 + - + +
153X LYS* 2.9 31.5 + - + -
154X LYS 3.3 8.1 - - - +
155X ASN* 3.6 27.6 + - - +
259X SER* 4.9 0.5 + - - -
261X SER* 4.8 0.7 + - - -
450X THR* 1.3 87.7 + - - +
452X TYR* 1.3 64.1 + - - +
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Residues in contact with TYR 452 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131X ILE* 3.7 10.6 - - - +
153X LYS* 3.6 3.8 - - - -
154X LYS* 2.9 69.9 + - + +
155X ASN 4.3 3.0 + - - -
156X ILE* 3.7 29.1 - - + +
258X TYR* 3.6 33.3 - + + -
259X SER* 3.7 24.2 - - - +
262X GLN* 3.7 21.8 + - + -
450X THR* 4.5 3.4 - - + +
451X GLU* 1.3 80.8 - - - +
453X VAL* 1.3 75.9 + - - +
454X GLU* 4.2 10.9 + - + +
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Residues in contact with VAL 453 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131X ILE* 3.7 33.3 - - + +
134X PHE* 4.6 14.6 - - + -
151X ARG* 3.6 36.6 - - + -
152X LYS 3.5 7.0 - - - +
153X LYS* 5.0 1.3 - - - -
258X TYR* 3.5 19.3 - - - +
259X SER* 5.9 0.4 - - - -
452X TYR* 1.3 80.2 - - - +
454X GLU* 1.3 60.7 + - - +
455X THR* 3.5 17.4 + - - +
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Residues in contact with GLU 454 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150X GLU 3.5 5.9 - - - +
152X LYS* 2.8 56.5 + - + +
154X LYS* 2.5 44.0 + - + +
258X TYR* 3.7 31.2 + - + +
362X GLU* 5.7 1.0 - - - +
452X TYR* 4.0 11.2 + - + -
453X VAL* 1.3 71.8 - - - +
455X THR* 1.3 58.2 + - - +
456X THR* 3.8 15.1 + - - +
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Residues in contact with THR 455 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149X ILE* 4.0 25.4 - - + -
150X GLU 3.4 4.3 - - - +
151X ARG* 4.2 6.8 + - + +
258X TYR* 3.8 22.4 + - - -
285X ILE* 4.0 24.3 - - - +
286X SER* 4.1 18.9 + - - +
288X GLY* 4.2 10.8 - - - -
291X LYS* 6.1 1.0 - - - +
453X VAL* 3.5 18.4 + - - +
454X GLU* 1.3 73.2 - - - +
456X THR* 1.3 66.8 + - - +
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Residues in contact with THR 456 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148X VAL 4.0 0.5 - - - +
149X ILE* 3.5 3.8 - - - +
150X GLU* 2.8 48.7 + - - +
258X TYR* 5.3 1.4 + - - -
291X LYS* 4.9 8.7 - - - +
358X SER 5.7 0.2 - - - +
359X ASN* 4.0 25.8 - - - +
454X GLU* 4.2 16.8 + - - +
455X THR* 1.3 78.3 + - - +
457X SER* 1.3 63.8 + - - +
458X THR* 5.4 0.4 - - - -
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Residues in contact with SER 457 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147X ILE* 4.0 4.2 - - - +
148X VAL 3.4 3.8 + - - -
149X ILE* 3.3 23.8 - - - +
288X GLY* 3.3 27.0 + - - -
291X LYS* 3.4 32.4 + - - +
357X LYS* 3.4 23.8 - - - +
358X SER 4.3 2.1 - - - +
359X ASN* 4.4 0.5 + - - -
456X THR* 1.3 80.3 - - - +
458X THR* 1.3 66.2 + - - +
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Residues in contact with THR 458 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147X ILE* 3.5 7.8 - - - +
148X VAL* 2.8 37.5 + - - +
357X LYS* 3.7 12.8 - - - +
359X ASN* 3.1 37.8 + - - +
456X THR* 5.3 0.5 - - - +
457X SER* 1.3 72.2 + - - +
459X GLU* 1.3 75.8 + - - +
460X TYR* 3.6 38.0 + - + +
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Residues in contact with GLU 459 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142X LYS* 5.6 0.2 - - - +
145X LYS* 3.6 44.2 - - + +
146X PHE 3.4 6.1 - - - +
147X ILE* 3.5 24.7 - - + +
357X LYS* 3.5 35.7 + - + +
458X THR* 1.3 83.0 - - - +
460X TYR* 1.3 75.3 + - - +
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Residues in contact with TYR 460 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145X LYS* 3.0 11.8 - - - +
146X PHE* 2.7 50.4 + + + +
148X VAL* 3.8 25.8 - - + -
359X ASN* 5.0 2.1 + - - -
458X THR* 3.6 29.4 + - + +
459X GLU* 1.3 80.7 - - - +
461X THR* 1.3 59.6 + - - +
484X ILE* 5.8 6.5 - - + -
518X ALA* 3.3 23.1 - - - +
549X LEU* 5.2 4.5 - - + -
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Residues in contact with THR 461 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144X ASP* 3.9 11.2 + - - -
145X LYS* 3.8 24.3 + - - -
460X TYR* 1.3 74.4 - - - +
462X SER* 1.3 73.6 + - - +
518X ALA* 3.6 3.4 - - - -
549X LEU* 3.2 32.4 - - - +
550X SER* 5.7 0.4 - - - -
551X LYS* 4.3 23.5 - - + +
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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