Contacts of the strand formed by residues 4028 - 4033 (chain D) in PDB entry 1D1Z
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 SER4028 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4020D LEU* 3.7 15.1 - - - +
4023D THR* 2.9 32.4 + - - +
4025D LEU* 3.1 28.1 + - - +
4026D ASP 3.3 1.0 + - - -
4027D GLY* 1.3 78.4 - - - +
4029D TYR* 1.3 61.0 + - - +
4045D VAL* 3.4 0.7 - - - -
4046D LEU* 2.9 29.3 + - - -
4100D TYR* 3.3 19.3 + - - +
4102D VAL* 4.7 1.5 - - - +
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Residues in contact with TYR4029 (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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4006D VAL* 4.0 20.9 - - + +
4020D LEU* 3.7 7.0 - - - +
4027D GLY 3.4 14.1 - - - +
4028D SER* 1.3 75.8 - - - +
4030D LEU* 1.3 67.7 + - - +
4043D LEU* 4.1 9.4 - - + -
4044D CYS 3.1 12.8 - - - +
4045D VAL* 4.2 2.2 - - + -
4084D ILE* 3.4 32.1 - - + +
4088D GLN* 3.7 10.9 + - - -
4098D LEU* 3.6 47.3 - - + -
4099D GLN 3.7 8.3 - - - -
4100D TYR 3.1 11.3 + - - -
4101D PRO* 3.5 35.3 - - + +
4102D VAL* 2.9 26.5 + - - +
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Residues in contact with LEU4030 (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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4006D VAL* 3.7 13.0 - - - +
4008D HIS* 4.2 9.2 - - - +
4011D ILE* 4.7 9.0 - - + -
4016D GLY* 3.8 31.4 - - - +
4019D LEU* 4.7 7.6 - - + -
4020D LEU* 4.0 17.3 - - + -
4029D TYR* 1.3 79.8 - - - +
4031D LEU* 1.3 73.1 - - - +
4032D ARG* 4.1 19.5 - - + -
4043D LEU* 3.6 8.8 - - - +
4044D CYS* 2.9 45.4 + - + -
4102D VAL* 4.2 17.9 - - + -
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Residues in contact with LEU4031 (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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4004D VAL* 5.0 3.6 - - + -
4006D VAL* 2.9 16.5 + - + +
4007D TYR* 3.9 32.5 - - + -
4008D HIS* 2.9 27.0 + - - +
4030D LEU* 1.3 77.1 - - - +
4032D ARG* 1.3 63.3 - - - +
4041D TYR* 4.2 24.9 - - + -
4042D CYS 3.4 15.9 - - - +
4043D LEU* 3.8 24.0 - - + +
4056D VAL* 4.3 11.2 - - + -
4064D TRP* 6.0 1.8 - - + -
4080D ILE* 4.2 27.4 - - + -
4083D LEU* 6.4 0.2 - - + -
4084D ILE* 5.3 4.9 - - + -
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Residues in contact with ARG4032 (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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4007D TYR* 4.3 2.2 - - - -
4008D HIS 3.6 15.5 - - - +
4011D ILE* 4.1 12.1 - - + +
4012D SER 4.0 19.0 - - - -
4013D ARG* 3.4 37.6 + - - +
4016D GLY* 4.9 3.7 - - - -
4017D GLU* 4.9 1.6 + - - +
4030D LEU* 4.1 12.3 - - + -
4031D LEU* 1.3 76.5 - - - +
4033D ASP* 1.3 78.0 + - - +
4035D GLU* 4.3 1.0 - - - +
4041D TYR* 3.3 10.7 - - - +
4042D CYS* 2.7 54.9 + - + +
4044D CYS* 3.4 16.8 - - - -
4053D THR* 3.9 10.7 + - - +
5004D SO4 2.8 43.9 + - - -
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Residues in contact with ASP4033 (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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4007D TYR* 2.6 29.5 + - - -
4008D HIS 4.3 1.2 + - - -
4009D GLY* 3.5 5.2 - - - -
4010D LYS* 3.2 31.5 + - - +
4011D ILE 4.6 8.2 + - - +
4032D ARG* 1.3 93.4 + - - +
4034D SER* 1.3 69.2 + - - +
4035D GLU* 3.5 4.0 + - - +
4040D VAL 4.0 5.8 - - - +
4041D TYR* 3.4 10.0 - - - -
4042D CYS 4.6 0.2 - - - -
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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