Contacts of the strand formed by residues 3221 - 3230 (chain D) in PDB entry 1G24
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 SER3221 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3167D ARG 3.7 0.9 - - - +
3168D LEU* 3.5 1.7 - - - +
3169D GLU* 2.9 30.3 + - - +
3171D GLY 5.2 0.2 + - - -
3173D ILE* 4.4 11.4 - - - -
3217D LEU* 5.2 0.9 - - - +
3218D PRO* 2.8 30.9 + - - +
3220D HIS* 1.3 78.7 - - - +
3222D THR* 1.3 61.7 + - - +
3223D TYR* 4.3 2.2 + - - -
3243D MET* 4.1 19.3 - - - -
3245D GLY 3.2 10.9 + - - -
3246D THR* 3.5 16.3 - - - +
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Residues in contact with THR3222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3166D ASP* 3.9 20.6 - - + +
3167D ARG 3.2 12.6 - - - +
3168D LEU* 3.6 20.0 - - + +
3220D HIS 4.2 0.9 + - - -
3221D SER* 1.3 71.9 - - - +
3223D TYR* 1.3 64.4 + - - +
3243D MET* 3.7 2.5 - - - +
3244D MET* 2.9 51.8 + - + +
3245D GLY 2.9 12.2 + - - -
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Residues in contact with TYR3223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3134D TYR* 2.7 33.2 + - - -
3165D LYS 3.9 0.5 - - - +
3166D ASP* 3.5 1.0 - - - -
3167D ARG* 2.8 69.6 + - + -
3169D GLU* 4.4 15.1 + - + -
3173D ILE* 4.2 15.7 - - + -
3190D THR* 5.7 0.9 - - + -
3192D PHE* 3.7 33.8 - + + -
3221D SER 4.6 2.0 - - - -
3222D THR* 1.3 75.8 - - - +
3224D HIS* 1.3 61.0 + - - +
3225D ILE* 4.2 12.3 - - + -
3239D ILE* 6.1 0.4 - - + -
3241D ALA* 3.9 11.9 - - + -
3242D THR 3.3 15.5 - - - +
3243D MET* 4.0 22.2 - - + -
3244D MET* 4.0 5.6 - - - +
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Residues in contact with HIS3224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3164D ASN* 3.3 42.6 + - - +
3165D LYS* 3.4 7.8 - - - -
3166D ASP* 2.8 25.0 + - - +
3223D TYR* 1.3 72.9 - - - +
3225D ILE* 1.3 64.5 + - - +
3226D ASP* 3.2 29.6 + - - +
3241D ALA* 3.1 4.9 - - - -
3242D THR* 2.8 42.4 + - - +
3244D MET* 3.9 9.8 - - + -
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Residues in contact with ILE3225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3134D TYR* 4.4 15.5 - - + +
3162D PHE* 3.6 44.6 - - + +
3163D LEU* 4.3 2.7 - - - -
3164D ASN* 2.9 32.6 + - - -
3165D LYS 3.3 10.0 + - - +
3167D ARG* 5.0 3.6 - - + -
3223D TYR* 4.2 17.9 - - + -
3224D HIS* 1.3 72.0 - - - +
3226D ASP* 1.3 59.7 + - - +
3227D ASP 4.1 3.6 - - - +
3228D MET* 3.6 33.7 - - + -
3239D ILE* 3.8 28.3 - - + -
3240D THR 3.8 2.9 - - - -
3241D ALA* 3.9 2.2 - - + -
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Residues in contact with ASP3226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3163D LEU* 3.8 9.8 - - - +
3164D ASN* 4.2 8.2 - - - +
3193D LYS* 4.9 5.5 + - - +
3224D HIS* 3.2 27.5 - - - +
3225D ILE* 1.3 74.3 - - - +
3227D ASP* 1.3 64.7 + - + +
3240D THR* 2.9 15.4 + - + +
3241D ALA* 3.8 3.5 - - - -
3242D THR* 2.7 36.4 + - - -
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Residues in contact with ASP3227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3163D LEU* 3.9 5.3 - - - +
3225D ILE 3.6 1.4 - - - -
3226D ASP* 1.3 81.4 - - + +
3228D MET* 1.3 79.4 + - - +
3229D ARG* 2.8 48.9 + - - +
3238D ILE 4.3 2.3 - - - +
3239D ILE* 3.4 1.2 - - - +
3240D THR* 2.8 48.3 + - + +
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Residues in contact with MET3228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3135D LEU* 4.6 7.9 - - + -
3155D PHE* 3.7 12.4 - - + -
3158D ALA* 4.0 26.5 - - + +
3159D LYS* 3.8 41.0 + - + +
3162D PHE* 4.1 7.2 - - + -
3163D LEU* 3.9 28.4 - - + +
3225D ILE* 3.6 17.9 - - + -
3227D ASP* 1.3 83.5 + - - +
3229D ARG* 1.3 63.3 + - - +
3237D ILE* 4.4 9.9 - - + -
3238D ILE 3.5 5.4 - - - +
3239D ILE* 4.1 28.3 - - + -
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Residues in contact with ARG3229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3155D PHE* 3.7 12.4 - - - -
3227D ASP* 2.8 37.8 + - - +
3228D MET* 1.3 74.1 - - - +
3230D LEU* 1.3 67.5 + - - +
3237D ILE* 3.6 0.4 - - - +
3238D ILE* 2.7 50.3 + - + +
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Residues in contact with LEU3230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3150D ILE* 3.4 52.0 - - + -
3152D LYS* 4.1 27.6 - - + +
3155D PHE* 3.7 26.4 - - + -
3229D ARG* 1.3 86.4 - - - +
3231D SER* 1.3 71.5 + - - +
3234D GLY 5.8 1.8 - - - +
3236D GLN 3.4 4.3 - - - +
3237D ILE* 4.0 6.5 - - + -
3238D ILE* 4.5 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