Contacts of the strand formed by residues 819 - 831 (chain I) in PDB entry 4XLN
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 VAL 819 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711I GLU* 3.9 16.6 - - + +
712I ALA 3.5 15.5 - - - +
713I ARG* 3.7 11.9 - - + +
714I ASP* 4.3 0.2 - - - -
808I ARG* 3.3 22.3 + - - +
815I LEU* 3.7 22.3 - - + +
816I LYS* 3.2 43.5 + - - +
817I PRO 3.8 4.3 - - - +
818I GLY* 1.3 84.5 - - - +
820I ARG* 1.3 65.4 + - - +
821I GLU 4.0 9.6 - - - +
532J GLY* 4.4 7.9 - - - +
320L GLU* 4.1 1.0 + - - -
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Residues in contact with ARG 820 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712I ALA 2.7 15.7 + - - +
713I ARG* 3.8 1.3 - - - +
714I ASP* 3.3 33.4 - - - +
719I PRO* 4.2 8.1 - - - -
720I GLU 3.4 25.4 + - - +
721I ARG* 3.6 37.3 - - - +
807I ARG* 3.8 9.7 - - - +
808I ARG* 2.8 43.9 + - + +
815I LEU* 3.2 6.7 - - - +
819I VAL* 1.3 71.2 - - - +
821I GLU* 1.3 75.9 + - + +
317L LYS* 5.5 4.4 - - - +
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Residues in contact with GLU 821 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710I ILE 4.4 0.2 - - - -
711I GLU* 3.3 1.0 - - - +
712I ALA* 2.9 33.0 + - + +
721I ARG* 3.5 21.0 - - - +
722I ILE* 3.3 32.3 - - + +
805I ARG* 3.0 33.2 + - - +
806I LEU 3.9 5.4 - - - +
807I ARG* 3.4 32.9 + - + +
815I LEU* 4.1 0.4 - - - -
819I VAL* 4.0 0.9 - - - +
820I ARG* 1.3 98.5 + - + +
822I VAL* 1.3 70.7 + - - +
823I VAL* 5.2 1.6 - - + -
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Residues in contact with VAL 822 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709I GLU* 6.2 1.3 - - + -
710I ILE 3.2 5.8 - - - +
711I GLU* 3.6 29.8 - - + -
804I LEU 4.0 0.9 - - - +
806I LEU* 2.8 67.3 + - + +
815I LEU* 3.7 31.2 - - + -
821I GLU* 1.3 80.0 - - - +
823I VAL* 1.3 64.0 + - - +
824I ARG* 4.3 10.3 - - + +
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Residues in contact with VAL 823 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708I TYR 3.5 2.1 - - - +
709I GLU* 3.2 2.1 - - - -
710I ILE* 2.9 43.6 + - + +
722I ILE* 4.1 19.7 - - + -
742I ILE* 3.9 14.8 - - + -
756I VAL* 3.6 26.3 - - + +
803I ARG* 4.7 6.3 - - + -
804I LEU 3.6 8.3 - - - +
805I ARG* 3.9 32.5 - - - +
821I GLU* 4.9 1.3 - - + +
822I VAL* 1.3 79.2 - - - +
824I ARG* 1.3 66.6 + - - +
825I VAL* 4.5 5.8 - - + -
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Residues in contact with ARG 824 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I ARG 3.6 5.7 + - - -
85I GLU* 3.0 30.2 + - - +
87I ASP* 2.7 36.6 + - - -
707I ARG* 3.1 41.8 - - + +
708I TYR 3.3 7.2 - - - +
709I GLU* 3.3 32.5 + - + -
803I ARG* 3.8 0.9 - - - -
804I LEU* 2.9 62.7 + - + +
806I LEU* 5.5 5.2 - - + +
822I VAL* 4.9 9.6 - - + -
823I VAL* 1.3 81.4 - - - +
825I VAL* 1.3 62.5 + - - +
826I PHE* 4.1 9.8 + - + -
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Residues in contact with VAL 825 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706I GLU 3.4 3.3 - - - +
707I ARG* 3.7 1.6 - - - -
708I TYR* 2.9 38.3 + - + +
743I VAL* 3.8 23.1 - - + +
755I LEU* 4.3 11.7 - - + -
756I VAL* 3.6 30.5 - - + -
800I VAL* 3.7 30.1 - - + -
802I GLY 3.8 3.6 - - - +
803I ARG* 4.7 9.6 - - + +
823I VAL* 4.5 4.7 - - + -
824I ARG* 1.3 75.5 - - - +
826I PHE* 1.3 65.2 + - - +
827I VAL* 4.0 11.7 - - + -
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Residues in contact with PHE 826 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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630I ARG* 4.5 21.8 - - + -
705I ILE* 4.1 12.6 - - + -
706I GLU 3.5 8.1 - - - -
707I ARG* 4.3 32.8 - - + -
800I VAL* 3.4 10.0 - - - +
801I VAL* 3.4 23.2 + - + +
802I GLY* 2.9 35.0 + - - +
803I ARG 4.9 0.7 - - - -
804I LEU* 5.4 20.0 - - + -
824I ARG* 5.2 8.1 - - + -
825I VAL* 1.3 76.4 - - - +
827I VAL* 1.3 62.3 + - - +
828I ALA 4.0 0.2 - - - -
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Residues in contact with VAL 827 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704I HIS 4.0 1.0 - - - +
705I ILE* 3.3 4.1 - - - +
706I GLU* 2.9 34.8 + - - +
708I TYR* 3.4 32.8 - - + +
749I VAL* 5.7 1.1 - - + -
755I LEU* 4.0 27.6 - - + -
792I VAL* 5.6 2.5 - - + -
797I GLY* 4.0 10.8 - - - +
798I GLY* 3.8 25.4 - - - +
799I ILE 3.4 16.4 - - - +
800I VAL* 4.4 1.8 - - + -
825I VAL* 4.0 7.6 - - + -
826I PHE* 1.3 75.3 - - - +
828I ALA* 1.3 59.9 - - - +
829I GLN* 4.4 5.9 - - + +
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Residues in contact with ALA 828 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G PHE* 4.3 12.3 - - + -
704I HIS 3.4 4.5 - - - +
705I ILE* 3.7 22.4 - - + +
798I GLY* 3.9 0.2 - - - -
799I ILE* 3.3 41.7 + - + +
801I VAL* 3.6 28.7 - - + -
826I PHE 3.9 1.8 + - - -
827I VAL* 1.3 70.9 - - - +
829I GLN* 1.3 66.4 + - - +
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Residues in contact with GLN 829 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G PHE* 5.0 4.0 - - - -
703I ILE* 3.6 5.2 - - - +
704I HIS* 2.8 36.0 + - - +
706I GLU* 5.8 2.1 - - - +
708I TYR* 4.7 4.3 + - - -
796I GLU* 3.6 12.5 - - - +
797I GLY* 3.1 45.0 + - - +
798I GLY* 5.2 1.3 - - - -
799I ILE* 5.6 0.2 - - - -
827I VAL* 4.4 7.5 - - + +
828I ALA* 1.3 78.7 - - - +
830I LYS* 1.3 63.3 + - - +
831I ARG* 3.4 27.6 + - - +
1002I GLU* 3.0 27.5 + - - -
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Residues in contact with LYS 830 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G GLU* 3.3 35.6 + - - +
65G PHE* 5.3 5.8 - - + -
76G VAL* 4.9 7.8 - - + +
153G ALA* 4.6 11.9 - - - +
154G GLU* 3.3 33.1 + - - +
166G PRO 5.2 1.6 + - - -
167G VAL* 5.7 1.0 - - - +
168G ASP* 4.6 13.5 + - - +
572I ILE* 4.4 10.1 - - + -
698I ASP* 5.4 3.3 + - - +
701I THR* 4.1 19.3 - - + -
702I SER 3.9 2.5 - - - -
703I ILE* 4.1 17.0 - - + -
829I GLN* 1.3 73.2 - - - +
831I ARG* 1.3 60.1 + - - +
832I LYS* 3.7 9.7 + - - +
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Residues in contact with ARG 831 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700I TYR 4.6 0.3 - - - +
701I THR* 3.3 3.0 - - - +
702I SER* 2.9 49.5 + - - +
704I HIS* 3.2 44.8 + - + +
795I GLY 5.1 3.0 + - - -
796I GLU* 5.1 3.6 - - - +
829I GLN* 3.4 39.1 + - + +
830I LYS* 1.3 71.9 - - - +
832I LYS* 1.3 62.1 + - - +
833I LEU 4.2 0.2 + - - -
996I LYS* 4.7 1.3 + - - -
1000I MET* 3.7 24.7 - - - -
1002I GLU* 3.3 38.9 + - - +
1003I ASP* 3.2 28.0 + - - -
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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