Contacts of the strand formed by residues 1041 - 1050 (chain B) in PDB entry 5FLM
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 ILE1041 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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684A GLY* 5.7 0.4 - - - -
685A HIS 4.8 4.7 - - - +
686A THR* 4.0 9.0 - - - -
781B ALA* 3.6 29.2 - - + -
782B ILE 3.3 18.4 - - - +
783B ALA* 3.6 20.4 - - + -
1025B ASN* 4.5 0.2 - - - -
1026B GLU* 3.0 31.2 + - - +
1028B LEU* 3.5 33.7 - - + -
1037B ILE* 3.5 37.0 - - + -
1039B SER* 3.5 7.6 - - - +
1040B GLN* 1.3 73.9 - - - +
1042B PHE* 1.3 64.9 + - - +
1043B ILE* 3.5 4.5 + - - +
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Residues in contact with PHE1042 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686A THR* 3.4 8.4 + - - +
687A ILE 3.6 20.6 - - - +
688A GLY* 4.0 4.9 - - - -
689A ILE* 4.3 14.1 - - + -
780B VAL 3.5 1.2 - - - +
781B ALA* 3.2 1.2 - - - -
782B ILE* 2.9 46.8 + - + -
981B LEU* 3.6 32.8 - - + -
984B CYS* 3.4 33.7 - - + -
985B LEU* 4.3 7.4 - - + -
1023B ARG 3.4 20.9 - - - -
1024B GLY* 3.7 26.2 - - - -
1025B ASN* 3.8 12.6 - - - +
1040B GLN 3.8 0.6 + - - -
1041B ILE* 1.3 74.0 - - - +
1043B ILE* 1.3 61.2 + - - +
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Residues in contact with ILE1043 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779B ILE* 3.8 20.6 - - + -
780B VAL 3.1 4.7 - - - +
781B ALA* 3.5 21.8 - - + -
957B THR* 3.7 15.9 - - + -
961B ILE* 5.5 3.6 - - + +
963B PRO* 5.4 5.2 - - + -
984B CYS* 4.1 5.5 - - - +
988B LYS* 3.5 19.4 + - - +
1024B GLY* 3.6 12.7 + - - +
1026B GLU* 3.7 15.0 - - + +
1028B LEU* 3.5 39.3 - - + -
1041B ILE 3.5 8.3 + - - +
1042B PHE* 1.3 77.8 - - - +
1044B GLY* 1.3 62.5 + - - +
43J TYR* 3.5 21.8 - - - +
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Residues in contact with GLY1044 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779B ILE* 4.5 1.8 - - - -
780B VAL* 2.9 30.6 + - - +
984B CYS* 3.4 24.0 - - - -
988B LYS* 4.4 3.8 - - - -
1043B ILE* 1.3 79.6 - - - +
1045B PRO* 1.3 75.9 - - - +
1046B THR 3.5 1.2 + - - -
43J TYR* 4.7 0.7 - - - -
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Residues in contact with PRO1045 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758B LEU* 4.0 22.2 - - + +
759B VAL* 5.8 0.3 - - - +
777B ASN* 5.2 2.2 - - + +
778B SER 2.9 17.3 - - - +
779B ILE* 3.9 12.1 - - + -
983B GLU* 4.3 1.9 - - - +
984B CYS* 3.9 10.9 - - - +
987B GLY* 3.5 30.2 - - - +
988B LYS* 3.8 17.0 - - - +
991B ALA* 4.7 0.4 - - + -
1044B GLY* 1.3 84.5 - - - +
1046B THR* 1.3 62.2 + - - +
43J TYR* 3.9 23.3 - - + -
47J ARG* 4.5 4.9 - - - -
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Residues in contact with THR1046 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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777B ASN* 4.3 3.6 - - - -
778B SER* 2.9 27.0 + - - -
780B VAL* 4.6 3.3 - - - +
937B SER* 4.8 2.2 - - - -
938B ARG 5.6 0.2 - - - +
980B HIS* 4.1 21.5 + - + +
983B GLU* 3.6 27.8 - - - +
984B CYS* 3.4 26.7 - - - +
1044B GLY 3.5 1.5 + - - -
1045B PRO* 1.3 77.5 + - - +
1047B TYR* 1.3 67.2 - - - +
1048B TYR* 3.2 36.2 - - + -
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Residues in contact with TYR1047 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755B GLN 3.0 30.0 + - - -
757B PRO* 4.0 10.8 - - + -
769B PHE* 3.9 18.0 - + - -
773B PRO* 3.7 2.4 - - - +
774B ALA 2.9 43.2 + - - -
775B GLY* 3.0 9.2 + - - -
776B ILE* 3.7 20.2 - - - -
777B ASN* 3.6 29.3 + - - +
937B SER* 4.0 0.7 - - - -
938B ARG* 3.5 66.0 + - + +
983B GLU* 3.7 1.8 + - - -
1046B THR* 1.3 78.4 - - - +
1048B TYR* 1.3 61.7 + - - +
1049B GLN* 4.3 8.1 - - + -
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Residues in contact with TYR1048 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775B GLY* 3.3 1.4 - - - -
776B ILE 2.9 35.9 + - - +
778B SER* 3.3 11.2 - - - +
780B VAL* 3.3 28.9 - - + +
794B VAL* 6.0 2.5 - - + -
806B PHE* 3.4 25.4 - - + -
935B PHE* 5.3 7.0 - - + -
936B ALA* 4.0 7.0 - - - -
937B SER* 3.5 28.7 - - - -
941B GLN* 5.2 2.5 - - + -
965B ILE* 4.3 11.4 - - + -
967B ILE* 3.7 24.6 - - + +
980B HIS* 2.8 31.9 + - - -
1046B THR* 3.2 35.7 - - + -
1047B TYR* 1.3 74.8 - - - +
1049B GLN* 1.3 61.9 + - - +
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Residues in contact with GLN1049 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710B ILE* 4.0 24.7 - - - +
725B GLN* 3.4 20.9 + - - +
728B MET 4.7 1.9 - - - +
729B GLY* 4.1 5.8 + - - -
732B ALA* 3.7 27.1 - - + +
769B PHE* 5.1 4.2 - - - -
774B ALA* 3.5 22.2 + - - +
775B GLY* 4.2 4.3 - - - -
806B PHE* 4.8 1.3 - - - -
935B PHE* 3.7 4.6 - - - +
936B ALA* 3.0 36.9 + - - +
937B SER 4.2 4.6 - - - +
938B ARG* 4.2 16.8 - - + +
1047B TYR* 4.3 10.5 - - + -
1048B TYR* 1.3 75.2 - - - +
1050B ARG* 1.3 61.6 + - - +
1051B LEU* 4.1 7.1 - - + +
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Residues in contact with ARG1050 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732B ALA* 3.3 7.1 - - - -
733B MET* 2.9 47.3 + - + +
751B LEU* 5.4 5.6 - - + +
775B GLY* 5.0 3.0 - - - -
806B PHE* 2.6 54.3 + - + -
808B SER* 3.4 21.3 + - - -
927B ARG* 3.4 25.9 + - - +
929B PRO* 3.7 7.2 - - - +
933B ASP* 2.6 31.9 + - + +
934B LYS 4.5 0.2 - - - +
935B PHE* 3.4 28.6 - - + -
1048B TYR 4.1 1.8 + - - -
1049B GLN* 1.3 72.5 - - - +
1051B LEU* 1.3 67.2 + - - +
1054B MET* 3.1 31.2 - - - +
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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