Contacts of the strand formed by residues 4016 - 4022 (chain D) in PDB entry 4O2W
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 ASN4016 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4003D GLY 3.8 3.3 + - - -
4004D ALA* 4.5 4.9 - - - +
4006D ARG* 3.0 43.5 + - - +
4015D ARG* 1.3 92.8 + - - +
4017D VAL* 1.3 63.3 + - - +
4018D MET* 4.3 4.6 + - + +
4320D GLU* 4.0 21.0 + - - -
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Residues in contact with VAL4017 (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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4001D LEU 3.9 8.5 - - - +
4002D TRP* 3.9 2.0 - - - -
4003D GLY* 2.8 43.6 + - - +
4010D LEU* 4.0 17.7 - - + -
4013D ALA* 3.3 27.6 - - + +
4014D GLY* 4.2 5.4 - - - -
4016D ASN* 1.3 79.0 - - - +
4018D MET* 1.3 62.1 + - - +
4019D VAL 3.0 26.0 - - - +
4021D ALA* 3.9 15.7 - - + -
4320D GLU 4.1 3.2 + - - +
4321D GLY 3.7 1.9 - - - +
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Residues in contact with MET4018 (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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4002D TRP* 4.8 0.2 - - - -
4016D ASN* 4.3 3.6 + - + +
4017D VAL* 1.3 77.2 - - - +
4019D VAL* 1.3 60.1 + - + +
4320D GLU 5.5 0.7 - - - +
4321D GLY* 4.1 9.7 - - - +
4324D GLY* 3.2 17.5 + - - -
4325D LEU 3.3 0.3 + - - -
4326D GLY* 2.9 46.8 + - - +
4327D HIS* 3.8 19.0 - - - +
4328D THR* 3.6 25.6 - - + +
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Residues in contact with VAL4019 (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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4002D TRP* 3.9 4.3 - - - -
4017D VAL* 3.0 20.0 - - - +
4018D MET* 1.3 86.1 - - + +
4020D PRO* 1.3 86.3 - - + +
4021D ALA* 4.0 0.9 - - - +
4324D GLY 4.1 3.6 - - - +
4325D LEU 4.6 1.1 - - - -
4326D GLY* 3.6 21.1 - - - +
4339D GLY* 4.9 11.7 - - - -
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Residues in contact with PRO4020 (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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4000D TYR* 4.1 8.0 - - + -
4001D LEU 3.9 0.2 - - - +
4002D TRP* 3.7 27.8 - - + -
4019D VAL* 1.3 97.3 - - + +
4021D ALA* 1.3 58.1 + - - +
4022D ALA 4.4 0.5 + - - -
4324D GLY* 3.4 23.1 - - - +
4337D VAL* 3.9 11.0 - - + -
4339D GLY* 4.4 12.1 - - - +
4340D LEU* 3.7 38.1 - - + -
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Residues in contact with ALA4021 (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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4000D TYR* 3.3 3.2 - - - -
4001D LEU* 2.9 40.0 + - - +
4013D ALA* 4.0 21.5 - - + +
4017D VAL* 3.9 17.5 - - + -
4019D VAL 4.0 0.7 - - - +
4020D PRO* 1.3 73.5 - - - +
4022D ALA* 1.3 66.9 + - - +
4023D ALA 3.4 0.3 + - - -
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Residues in contact with ALA4022 (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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3998D ASP* 6.4 0.9 - - + -
3999D VAL 3.4 8.5 - - - +
4000D TYR* 3.7 21.7 - - + -
4012D GLU* 5.3 0.5 - - - +
4013D ALA* 4.2 11.6 + - - +
4020D PRO 4.4 0.4 + - - -
4021D ALA* 1.3 74.1 - - - +
4023D ALA* 1.3 59.0 + - - +
4024D PRO* 3.5 15.4 - - + +
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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