Contacts of the strand formed by residues 776 - 782 (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 ILE 776 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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751B LEU* 4.0 11.4 - - + -
753B TYR* 3.2 24.7 - - + +
755B GLN* 3.5 19.3 - - - +
775B GLY* 1.3 80.2 - - - +
777B ASN* 1.3 77.4 + - - +
778B SER 3.9 0.3 + - - -
804B GLY 4.8 1.3 - - - +
805B PHE* 3.7 16.4 - - + -
806B PHE* 3.5 48.2 - - + +
1047B TYR* 3.7 8.6 - - - -
1048B TYR* 2.9 32.1 + - - +
8J PHE* 4.1 14.6 - - + -
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Residues in contact with ASN 777 (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* 3.1 25.8 + - - +
756B LYS 3.3 24.9 + - - -
758B LEU* 3.5 36.3 + - + +
776B ILE* 1.3 85.4 - - - +
778B SER* 1.3 58.3 + - - +
805B PHE* 3.7 1.9 - - - -
938B ARG* 5.5 0.2 + - - -
1045B PRO* 5.2 1.9 - - + +
1046B THR* 3.7 5.8 + - - +
1047B TYR* 3.6 27.6 + - - +
47J ARG* 2.7 29.3 + - + +
51J ALA* 3.4 11.0 - - + +
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Residues in contact with SER 778 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
776B ILE 4.7 1.3 - - - -
777B ASN* 1.3 78.6 - - - +
779B ILE* 1.3 63.6 + - - +
780B VAL* 3.4 9.4 + - - +
805B PHE* 3.7 24.5 - - - -
964B ASP* 4.0 8.7 - - - -
965B ILE* 3.7 6.6 - - - +
1045B PRO* 2.9 24.0 - - - +
1046B THR 2.9 11.5 + - - -
1048B TYR* 3.3 26.3 - - - -
47J ARG* 3.8 7.6 - - - +
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Residues in contact with ILE 779 (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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778B SER* 1.3 71.1 - - - +
780B VAL* 1.3 59.9 + - - +
961B ILE* 3.9 18.4 - - + -
962B THR 4.3 0.9 - - - +
963B PRO* 3.3 11.8 - - + +
964B ASP* 2.8 35.5 + - - +
965B ILE 3.2 7.6 + - - -
1043B ILE* 3.8 24.0 - - + -
1044B GLY 4.0 2.0 - - - +
1045B PRO* 3.9 9.6 - - + -
9J THR* 3.5 24.5 - - + +
43J TYR* 3.5 29.6 - - + +
44J CYS* 4.2 9.0 - - + -
47J ARG* 3.5 25.8 - - - +
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Residues in contact with VAL 780 (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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778B SER* 3.4 20.0 - - - +
779B ILE* 1.3 74.8 - - - +
781B ALA* 1.3 70.4 + - - +
782B ILE* 4.4 4.9 - - + -
963B PRO* 4.4 0.4 - - - -
965B ILE* 3.2 20.2 - - + +
967B ILE* 4.1 17.3 - - + -
980B HIS* 5.0 2.7 - - + -
984B CYS* 4.4 4.4 - - - -
1042B PHE 3.5 1.7 - - - +
1043B ILE* 3.1 5.1 - - - -
1044B GLY 2.9 38.2 + - - +
1046B THR* 4.6 4.0 - - - +
1048B TYR* 3.3 44.4 - - + +
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Residues in contact with ALA 781 (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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780B VAL* 1.3 72.1 - - - +
782B ILE* 1.3 62.9 + - - +
783B ALA* 3.5 3.2 + - + -
955B PRO* 5.6 0.2 - - + -
963B PRO* 3.7 24.1 - - + +
965B ILE 3.4 4.4 + - - -
966B ILE* 3.4 29.0 - - + +
967B ILE 3.6 1.6 + - - -
1028B LEU* 4.2 5.2 - - + -
1041B ILE* 3.6 14.4 - - + -
1042B PHE 3.2 5.4 - - - -
1043B ILE* 3.5 22.9 - - + -
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Residues in contact with ILE 782 (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* 2.7 27.9 + - - +
687A ILE* 4.1 14.4 - - + +
780B VAL* 4.4 5.8 - - + +
781B ALA* 1.3 69.6 - - - +
783B ALA* 1.3 64.4 + - - +
967B ILE* 3.5 35.4 - - + +
968B ASN 4.4 0.9 - - - -
969B PRO* 3.6 33.9 - - + -
972B ILE* 5.0 5.8 - - + -
980B HIS* 4.3 10.5 - - + +
981B LEU* 3.6 31.0 - - + -
984B CYS* 5.4 1.8 - - - -
1041B ILE* 3.3 3.1 - - - +
1042B PHE* 2.9 28.1 + - + +
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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