Contacts of the strand formed by residues 4254 - 4266 (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 VAL4254 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4244D MSE 3.7 28.7 - - - +
4247D LEU* 3.7 13.7 - - + -
4248D ARG* 3.6 39.9 + - + +
4252D PHE* 3.4 16.1 + - + +
4253D ASP* 1.3 70.6 - - - +
4255D ASN* 1.3 75.5 + - - +
4282D ILE* 3.4 31.0 - - + -
4283D TYR 3.8 5.6 - - - +
4284D THR* 4.8 0.9 - - + +
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Residues in contact with ASN4255 (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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1264A GLY 5.6 3.8 - - - +
4244D MSE 5.2 0.2 - - - -
4253D ASP* 3.8 10.9 + - - +
4254D VAL* 1.3 84.1 + - - +
4256D ILE* 1.3 63.2 + - - +
4282D ILE* 3.3 6.6 - - - +
4283D TYR* 2.9 75.8 + - + +
4285D GLY* 4.3 8.7 - - - +
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Residues in contact with ILE4256 (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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1262A ALA 4.1 0.2 - - - +
1263A ARG* 3.4 2.9 - - - +
1264A GLY* 2.9 35.7 + - - +
1271A THR* 4.1 21.1 - - + -
1273A MSE 4.2 16.8 - - + +
2237B LEU* 4.2 22.2 - - + -
4240D LYS* 4.5 7.6 - - + -
4244D MSE 3.7 21.8 - - + -
4255D ASN* 1.3 78.4 - - - +
4257D THR* 1.3 72.3 + - - +
4258D GLU* 4.8 4.3 - - + +
4280D ALA* 4.0 20.6 - - + -
4281D LEU 3.3 10.5 - - - +
4282D ILE* 4.1 15.5 - - + -
4283D TYR* 4.4 0.6 + - - -
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Residues in contact with THR4257 (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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1120A GLU* 3.9 23.5 + - - +
1261A ILE* 3.9 13.5 - - + -
1262A ALA 3.2 10.5 - - - +
1263A ARG* 4.2 7.7 - - + +
4124D LEU* 4.4 12.6 - - + -
4128D LEU* 6.1 0.4 - - - -
4256D ILE* 1.3 79.1 + - - +
4258D GLU* 1.3 61.8 + - - +
4259D LEU* 4.1 14.4 + - + +
4279D VAL 3.9 0.7 - - - +
4280D ALA* 3.4 1.0 - - - -
4281D LEU* 3.0 38.0 + - - +
4283D TYR* 3.8 21.1 + - - -
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Residues in contact with GLU4258 (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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1260A ASN 3.8 1.9 - - - +
1261A ILE* 3.6 1.9 - - - -
1262A ALA* 2.8 34.7 + - + +
1273A MSE 3.9 23.5 - - + +
2237B LEU* 5.5 2.9 - - - +
2240B LYS* 5.4 3.5 + - - -
2258B GLU* 4.8 9.1 - - - +
4240D LYS* 2.9 41.9 + - - +
4256D ILE* 4.8 4.0 - - + +
4257D THR* 1.3 73.6 - - - +
4259D LEU* 1.3 65.2 + - - +
4260D ASN* 4.5 8.9 + - - +
4278D PRO* 3.6 21.3 - - - +
4279D VAL 3.4 6.4 + - - +
4280D ALA* 3.9 12.3 - - + -
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Residues in contact with LEU4259 (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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1120A GLU* 4.7 4.5 - - + -
1259A LEU* 5.7 9.6 - - + -
1260A ASN 3.9 0.9 - - - +
1261A ILE* 3.7 31.9 - - + -
4120D GLU* 4.3 15.0 - - + +
4121D VAL* 4.0 25.1 - - + -
4124D LEU* 4.0 25.4 - - + -
4257D THR* 4.2 8.7 - - + +
4258D GLU* 1.3 80.8 - - - +
4260D ASN* 1.3 62.2 + - - +
4261D ILE* 3.9 17.5 + - + +
4277D ASN 4.4 1.6 - - - +
4278D PRO* 3.5 5.2 - - - +
4279D VAL* 2.8 36.3 + - - +
4281D LEU* 5.5 3.6 - - + -
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Residues in contact with ASN4260 (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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1258A GLU 3.7 2.4 - - - +
1259A LEU* 3.9 0.5 - - - -
1260A ASN* 2.9 55.4 + - + +
1262A ALA* 6.4 0.4 - - - +
2260B ASN* 4.1 24.4 + - - +
3260C ASN* 5.3 13.7 - - - +
3262C ALA* 5.5 1.2 - - - +
3275C SER* 4.0 8.3 + - - -
4258D GLU* 4.5 10.3 + - - +
4259D LEU* 1.3 77.7 + - - +
4261D ILE* 1.3 60.6 + - - +
4276D ARG 4.7 3.1 - - - +
4278D PRO* 3.5 32.0 - - - +
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Residues in contact with ILE4261 (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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1257A THR* 3.8 26.2 - - + -
1258A GLU 3.5 3.6 - - - +
1259A LEU* 3.7 15.5 - - + -
4118D ALA* 4.2 8.7 - - + -
4120D GLU* 3.5 39.0 - - + +
4121D VAL* 4.1 22.0 - - + -
4259D LEU* 3.9 12.2 + - + +
4260D ASN* 1.3 79.1 - - - +
4262D ALA* 1.3 66.0 + - - +
4263D ARG* 4.2 8.3 - - + +
4275D SER* 3.6 3.0 - - - -
4276D ARG* 2.9 43.1 + - + +
4277D ASN 5.8 0.6 + - - +
4279D VAL* 6.0 1.6 - - + -
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Residues in contact with ALA4262 (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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1257A THR* 3.3 3.6 - - - +
1258A GLU* 2.7 41.8 + - + +
1260A ASN* 6.4 0.4 - - - +
3260C ASN* 5.7 0.9 - - - +
3278C PRO* 4.2 16.6 - - + -
4261D ILE* 1.3 75.8 - - - +
4263D ARG* 1.3 61.1 + - - +
4273D MSE 3.4 28.5 - - + +
4274D VAL 3.1 12.1 - - - +
4275D SER* 4.5 2.2 - - - +
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Residues in contact with ARG4263 (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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1256A ILE 3.3 7.9 - - - +
1257A THR* 4.1 11.4 - - - +
1283A TYR* 6.0 1.3 - - - -
4104D ASP* 3.1 36.0 + - - +
4118D ALA* 3.5 14.3 - - - +
4119D MSE 3.8 3.8 - - - +
4120D GLU* 2.8 35.9 + - - +
4261D ILE* 4.2 7.6 - - + +
4262D ALA* 1.3 77.5 - - - +
4264D GLY* 1.3 66.3 + - - +
4265D ARG 3.7 0.2 + - - -
4273D MSE 3.9 2.9 - - - -
4274D VAL* 2.8 36.1 + - + +
4276D ARG* 3.3 42.6 - - + +
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Residues in contact with GLY4264 (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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1255A ASN* 5.7 3.5 - - - +
1256A ILE* 2.8 25.9 + - - +
4263D ARG* 1.3 76.1 - - - +
4265D ARG* 1.3 61.1 + - - -
4266D ALA 4.1 1.4 + - - -
4271D THR* 3.8 18.4 - - - -
4272D MSE 3.3 7.2 - - - -
4273D MSE 3.9 5.7 - - - +
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Residues in contact with ARG4265 (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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4263D ARG 3.7 0.2 + - - -
4264D GLY* 1.3 72.5 - - - -
4266D ALA* 1.3 71.3 + - - +
4267D LEU* 3.3 21.5 + - + +
4271D THR* 3.4 4.0 - - - -
4272D MSE 2.7 62.8 + - + +
4274D VAL* 3.8 39.2 - - + +
4276D ARG* 5.8 2.4 - - - +
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Residues in contact with ALA4266 (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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1248A ARG* 5.6 11.0 - - - +
1254A VAL 6.1 0.7 - - - +
4264D GLY 4.1 2.0 + - - -
4265D ARG* 1.3 74.1 - - - +
4267D LEU* 1.3 69.6 + - - +
4270D GLY 4.0 2.9 - - - -
4271D THR* 4.7 7.1 - - + +
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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