Contacts of the helix formed by residues 4164 - 4178 (chain D) in PDB entry 1F38
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 ASN4164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4112D SER* 3.5 26.5 + - - -
4113D VAL* 3.6 14.5 - - - +
4114D PRO* 5.3 2.2 - - - +
4162D ASP* 3.0 14.8 + - - +
4163D ARG* 1.3 78.3 - - - +
4165D PRO* 1.3 70.8 - - - +
4166D GLU* 2.9 31.2 + - - +
4167D ALA* 3.1 20.1 + - + +
4168D ILE* 3.3 8.8 + - - +
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Residues in contact with PRO4165 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4163D ARG 3.2 9.8 - - - +
4164D ASN* 1.3 89.1 - - - +
4166D GLU* 1.3 63.6 + - + +
4168D ILE* 3.2 5.0 + - + +
4169D SER* 2.9 29.0 + - - -
4188D GLU* 3.4 38.3 - - + +
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Residues in contact with GLU4166 (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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4110D ASN* 4.0 16.8 + - - +
4112D SER* 3.4 21.9 + - - +
4113D VAL* 3.4 17.0 - - + -
4164D ASN* 2.9 17.0 + - - +
4165D PRO* 1.3 82.8 - - + +
4167D ALA* 1.3 54.2 + - - +
4169D SER* 3.3 8.9 + - - -
4170D THR* 2.6 37.2 + - - -
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Residues in contact with ALA4167 (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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4113D VAL* 3.3 15.0 - - + +
4114D PRO* 6.1 0.2 - - + -
4142D CYS* 4.9 1.1 - - - -
4143D GLY* 3.1 24.3 - - - +
4162D ASP* 3.1 32.1 - - + +
4164D ASN* 3.1 17.6 + - + +
4166D GLU* 1.3 76.8 - - - +
4168D ILE* 1.3 65.9 + - - +
4170D THR 3.1 1.7 + - - -
4171D THR* 2.8 23.8 + - - -
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Residues in contact with ILE4168 (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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4142D CYS* 4.5 6.3 - - - -
4160D ALA 4.3 4.9 - - - +
4161D ILE 4.4 0.7 - - - -
4162D ASP* 3.9 17.9 - - + +
4164D ASN 3.8 10.8 - - - +
4165D PRO* 3.2 8.7 + - + +
4167D ALA* 1.3 78.1 - - - +
4169D SER* 1.3 58.4 + - - +
4171D THR* 3.5 6.6 + - - -
4172D GLU* 3.1 26.7 + - - +
4186D LEU* 3.8 25.1 - - + +
4187D MSE 3.5 34.5 - - - +
4188D GLU* 3.8 30.3 - - + +
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Residues in contact with SER4169 (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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4165D PRO 2.9 13.5 + - - -
4166D GLU* 3.3 14.4 - - - -
4168D ILE* 1.3 75.8 - - - +
4170D THR* 1.3 59.4 + - - +
4172D GLU* 3.2 8.8 + - - +
4173D MSE 3.0 42.6 + - - +
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Residues in contact with THR4170 (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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4108D ILE* 3.0 32.3 - - + +
4109D LYS* 4.6 1.8 - - - -
4110D ASN* 3.7 26.8 + - + +
4113D VAL* 4.1 3.3 - - + +
4143D GLY 4.4 5.8 - - - -
4144D THR* 3.9 10.8 - - + +
4166D GLU 2.6 26.4 + - - -
4167D ALA* 3.7 4.3 - - - -
4169D SER* 1.3 74.3 + - - +
4171D THR* 1.3 57.8 + - - +
4173D MSE 3.6 17.8 - - + +
4174D ASN* 2.9 39.7 + - - +
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Residues in contact with THR4171 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4142D CYS* 3.4 16.3 - - - -
4143D GLY 2.8 24.6 + - - -
4144D THR 3.6 7.0 - - - -
4145D GLY* 3.3 20.9 - - - +
4148D THR* 4.1 16.8 - - + -
4149D LEU* 4.5 0.4 - - + +
4167D ALA 2.8 11.2 + - - -
4168D ILE* 3.6 4.7 - - - -
4170D THR* 1.3 74.9 - - - +
4172D GLU* 1.3 55.6 + - - +
4174D ASN* 3.2 2.6 + - - +
4175D LEU* 2.8 54.3 + - + +
4186D LEU* 4.2 10.5 - - + -
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Residues in contact with GLU4172 (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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4168D ILE 3.1 9.1 + - - +
4169D SER* 3.5 10.5 - - - +
4171D THR* 1.3 74.8 - - - +
4173D MSE 1.3 63.4 + - + +
4175D LEU* 3.1 25.0 + - - +
4176D GLN* 3.0 47.4 + - - +
4180D LEU 5.3 0.2 - - - +
4181D GLY* 5.3 4.7 - - - +
4186D LEU* 3.6 27.3 - - + +
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Residues in contact with MSE4173 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4108D ILE* 4.4 20.6 - - + -
4110D ASN* 6.1 2.7 - - + +
4169D SER* 3.0 25.2 + - - +
4170D THR* 3.6 33.2 - - + +
4172D GLU* 1.3 78.2 - - + +
4174D ASN* 1.3 63.0 + - - +
4176D GLN* 3.0 21.7 + - - +
4177D ARG* 3.1 48.9 + - - +
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Residues in contact with ASN4174 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4106D GLU 4.4 2.6 - - - +
4107D PHE* 3.6 16.0 - - + -
4108D ILE* 2.9 52.5 + - - +
4144D THR* 3.0 32.3 + - - +
4149D LEU* 3.7 13.6 - - + +
4170D THR* 2.9 20.2 + - - +
4171D THR 3.7 2.9 - - - +
4173D MSE 1.3 73.6 - - - +
4175D LEU* 1.3 65.8 + - - +
4176D GLN 3.3 0.2 + - - -
4177D ARG* 3.6 3.0 + - - +
4178D HIS* 3.0 33.6 + - + -
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Residues in contact with LEU4175 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4148D THR* 4.5 7.2 - - + -
4149D LEU* 3.8 25.4 - - + -
4152D ALA* 4.5 0.9 - - + -
4171D THR* 2.8 34.4 + - + +
4172D GLU* 3.2 28.7 - - - +
4174D ASN* 1.3 76.1 - - - +
4176D GLN* 1.3 60.1 + - + +
4178D HIS* 3.4 1.6 + - - +
4179D GLY 2.9 8.0 + - - -
4180D LEU* 2.8 56.1 + - + +
4181D GLY* 4.0 11.2 - - - +
4184D VAL* 4.1 29.2 - - + -
4186D LEU* 4.2 4.3 - - + -
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Residues in contact with GLN4176 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4172D GLU* 3.0 42.3 + - - +
4173D MSE 3.3 13.6 - - - +
4175D LEU* 1.3 73.7 - - + +
4177D ARG* 1.3 66.7 + - - +
4178D HIS 2.7 6.4 + - - -
4179D GLY* 2.7 25.2 + - - +
4180D LEU 4.6 3.4 - - - +
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Residues in contact with ARG4177 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4108D ILE* 3.5 30.0 - - + +
4173D MSE 3.1 49.1 + - - +
4174D ASN* 3.6 3.1 + - - +
4176D GLN* 1.3 82.7 + - - +
4178D HIS* 1.3 78.8 + - + +
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Residues in contact with HIS4178 (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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4102D ILE* 3.7 29.7 - - + +
4106D GLU* 2.8 39.4 + - + -
4107D PHE* 5.0 2.8 - + - -
4149D LEU* 3.8 24.2 - - + -
4174D ASN* 3.0 32.2 + - + +
4175D LEU 3.4 1.4 + - - +
4176D GLN 2.8 1.0 - - - -
4177D ARG* 1.3 92.3 + - + +
4179D GLY* 1.3 63.5 + - - +
4180D LEU* 3.6 12.1 - - + +
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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