Contacts of the helix formed by residues 301 - 312 (chain 5) in PDB entry 1SVA
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 ILE 301 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1045 CYS* 5.8 10.5 - - - -
2975 ASN* 5.0 2.5 - - - +
2995 TYR 4.1 0.4 + - - -
3005 PRO* 1.3 81.4 - - + +
3025 SER* 1.3 79.9 + - - +
3045 LEU* 2.7 18.6 + - + +
3055 LEU* 2.6 42.8 + - + +
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Residues in contact with SER 302 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3005 PRO* 2.9 6.8 + - - +
3015 ILE* 1.3 89.7 - - - +
3035 PHE* 1.3 55.7 + - - +
3055 LEU* 3.6 5.5 - - - +
3065 SER* 2.5 35.7 + - - -
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Residues in contact with PHE 303 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2995 TYR* 4.0 38.6 - + + -
3005 PRO* 2.5 28.1 + - + +
3025 SER* 1.3 73.3 - - - +
3045 LEU* 1.3 75.0 + - + +
3065 SER* 3.0 6.9 + - - -
3075 ASP* 2.6 62.9 + - + +
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Residues in contact with LEU 304 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2975 ASN* 3.8 28.3 - - - +
2995 TYR* 3.9 26.5 - - + -
3005 PRO 2.9 4.1 + - - +
3015 ILE* 2.7 33.7 + - + +
3035 PHE* 1.3 77.1 - - + +
3055 LEU* 1.3 52.9 + - - +
3075 ASP* 4.2 1.5 - - - +
3085 LEU* 2.7 42.5 + - + +
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Residues in contact with LEU 305 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3015 ILE* 2.6 23.8 + - + +
3025 SER* 3.6 5.6 - - - +
3045 LEU* 1.3 72.8 - - - +
3065 SER* 1.3 54.1 + - - +
3085 LEU* 3.4 6.0 - - + +
3095 ILE* 2.6 68.8 + - + +
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Residues in contact with SER 306 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3025 SER 2.5 22.4 + - - -
3035 PHE* 3.0 15.8 + - - -
3055 LEU* 1.3 78.4 - - - +
3075 ASP* 1.3 52.5 + - - +
3095 ILE* 3.5 8.3 - - - +
3105 ASN* 2.5 39.1 + - - +
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Residues in contact with ASP 307 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3035 PHE* 2.6 57.8 + - + +
3045 LEU* 4.2 1.6 - - - +
3065 SER* 1.3 74.2 + - - +
3085 LEU* 1.3 51.5 + - - +
3105 ASN* 3.2 9.8 + - - +
3115 ARG* 2.7 73.2 + - - +
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Residues in contact with LEU 308 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3045 LEU* 2.7 27.0 + - + +
3055 LEU* 3.4 6.7 - - + +
3075 ASP* 1.3 72.8 - - - +
3095 ILE* 1.3 54.5 + - + +
3115 ARG* 2.7 16.0 + - + +
3125 ARG* 2.7 61.1 + - + +
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Residues in contact with ILE 309 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3055 LEU* 2.6 52.4 + - + +
3065 SER* 3.5 6.7 - - - +
3085 LEU* 1.3 74.9 - - + +
3105 ASN* 1.3 56.2 + - - +
3125 ARG* 3.2 8.6 + - - +
3135 THR* 2.7 45.7 + - - +
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Residues in contact with ASN 310 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3065 SER* 2.5 22.7 + - - +
3075 ASP* 3.3 16.4 - - - +
3095 ILE* 1.3 76.5 - - - +
3115 ARG* 1.3 73.0 + - - +
3135 THR* 2.8 29.6 + - - +
3145 GLN 5.5 3.0 + - - -
3155 ARG* 5.6 7.5 - - - +
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Residues in contact with ARG 311 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3075 ASP* 2.7 55.6 + - - +
3085 LEU* 2.7 16.6 + - + +
3105 ASN* 1.3 82.5 + - - +
3125 ARG* 1.3 62.8 + - + +
3135 THR 3.7 4.3 - - - +
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Residues in contact with ARG 312 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3085 LEU* 2.7 46.1 + - + +
3095 ILE* 3.5 9.0 - - - +
3115 ARG* 1.3 75.4 - - - +
3135 THR* 1.3 60.2 + - - +
3145 GLN 4.0 0.3 + - - -
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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