Contacts of the strand formed by residues 348 - 355 (chain A) in PDB entry 3HOU
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 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A VAL* 2.9 24.5 + - - -
346A ASP 4.1 1.3 - - - -
347A PHE* 1.3 75.1 - - - +
349A ALA* 1.3 62.4 + - - +
374A LEU* 3.6 3.1 - - - +
489A LEU 3.2 11.4 - - - -
490A HIS* 3.8 20.0 - - - -
1104B HIS* 6.0 0.3 - - - -
1105B ALA* 3.7 0.3 - - - -
1106B ARG* 2.9 30.5 + - - +
1127B GLY* 4.0 2.9 - - - -
1128B LEU* 3.3 26.7 + - - +
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Residues in contact with ALA 349 (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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348A SER* 1.3 77.3 - - - +
350A ARG* 1.3 64.3 + - - +
370A ILE* 3.9 10.8 - - + -
374A LEU* 3.5 20.4 - - + -
468A PHE* 3.9 5.6 - - + -
487A MET 3.9 0.3 - - - +
488A ASN* 3.4 1.4 - - - -
489A LEU* 2.9 35.2 + - + +
1104B HIS* 3.4 14.6 - - - +
1105B ALA* 3.5 15.7 - - + +
1128B LEU* 3.4 5.8 - - - +
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Residues in contact with ARG 350 (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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201 G 5.1 10.1 + - - +
211 C 3.6 36.2 + - - -
349A ALA* 1.3 76.0 - - - +
351A THR* 1.3 73.7 + - - +
447A GLN* 3.9 14.3 + - - -
468A PHE* 3.7 2.0 - - - -
486A GLU* 3.1 54.6 + - + +
487A MET* 3.4 9.1 - - - +
488A ASN* 2.8 40.0 + - - +
1102B LYS 4.0 1.9 - - - +
1103B ILE* 3.6 0.5 - - - -
1104B HIS* 2.8 34.5 + - + +
1128B LEU* 3.2 29.6 - - + +
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Residues in contact with THR 351 (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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350A ARG* 1.3 87.0 - - - +
352A VAL* 1.3 77.0 + - - +
353A ILE 3.6 0.2 + - - -
367A PRO* 4.8 1.1 - - + +
370A ILE* 3.7 15.7 - - + -
466A SER 3.4 13.8 + - - -
468A PHE* 3.2 23.3 + - - -
486A GLU* 3.4 13.0 - - - +
487A MET 3.3 20.0 + - - -
1099B VAL* 4.7 0.7 - - - -
1103B ILE* 3.1 47.8 - - + +
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Residues in contact with VAL 352 (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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351A THR* 1.3 89.8 + - - +
353A ILE* 1.3 73.5 + - - +
354A SER* 5.8 0.2 - - - -
467A THR* 3.2 28.0 - - + -
468A PHE 3.2 3.3 + - - -
484A GLY* 4.3 21.1 - - - +
485A ASP 3.5 12.8 - - - +
486A GLU* 3.6 3.5 - - + +
977B GLY* 3.8 18.8 - - - +
989B THR* 4.4 4.9 - - + +
1099B VAL* 4.1 18.8 - - + +
1102B LYS* 4.0 27.3 - - + +
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Residues in contact with ILE 353 (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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351A THR 3.6 7.4 - - - +
352A VAL* 1.3 91.6 - - - +
354A SER* 1.3 66.7 + - - +
444A PHE* 4.5 0.9 - - + -
468A PHE* 3.2 19.5 - - + +
470A LEU* 3.8 11.9 - - + -
480A ALA* 3.6 28.0 - - + -
481A ASP 4.3 5.6 - - - +
482A PHE* 3.6 28.8 - - + +
485A ASP* 3.1 14.4 + - + +
487A MET* 3.0 48.0 - - + +
989B THR* 4.2 2.1 + - - -
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Residues in contact with SER 354 (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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353A ILE* 1.3 78.8 - - - +
355A GLY* 1.3 66.7 + - - +
467A THR* 3.2 16.9 + - - -
468A PHE 3.1 4.6 + - - -
469A ARG* 3.1 48.1 + - - +
470A LEU* 3.6 1.5 + - - -
482A PHE* 3.4 12.1 - - - -
838B SER* 5.0 2.9 - - - -
976B ILE* 4.3 2.1 - - - +
977B GLY* 6.1 0.2 - - - -
989B THR* 4.6 4.5 - - - -
990B ILE 4.1 18.2 - - - -
991B GLY* 4.2 5.8 - - - -
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Residues in contact with GLY 355 (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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354A SER* 1.3 75.8 - - - +
356A ASP* 1.3 57.6 + - - -
357A PRO* 4.2 5.6 - - - +
469A ARG* 3.1 15.1 + - - -
470A LEU 3.3 10.1 - - - -
472A LEU* 4.9 7.0 - - - -
482A PHE* 3.0 36.5 - - - -
832B GLY 5.9 0.4 - - - -
833B TYR* 4.3 9.5 - - - +
838B SER* 4.9 2.7 + - - -
991B GLY* 4.9 1.2 - - - +
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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