Contacts of the strand formed by residues 819 - 832 (chain M) in PDB entry 2PPB
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 M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711M GLU* 4.1 13.0 - - + +
712M ALA 3.9 3.4 - - - +
713M ARG* 3.8 22.0 - - - +
815M LEU* 3.1 25.2 - - + +
816M LYS* 3.4 46.7 - - + +
817M PRO 2.7 13.7 + - - +
818M GLY* 1.3 69.9 + - - +
820M ARG* 1.3 63.3 + - - +
821M GLU 3.8 13.5 - - - +
822M VAL* 3.7 29.8 - - + -
532N GLY* 5.4 0.4 - - - -
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Residues in contact with ARG 820 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712M ALA* 2.7 28.2 + - + +
713M ARG 4.8 2.9 - - - -
714M ASP* 4.9 5.2 - - + +
719M PRO* 3.9 27.1 - - - +
720M GLU 3.7 19.6 + - - +
721M ARG* 3.8 32.2 - - - +
722M ILE* 4.4 11.5 - - - +
806M LEU 4.6 0.7 - - - +
807M ARG 4.8 0.3 - - - -
808M ARG* 4.8 35.0 + - + +
815M LEU* 3.6 13.8 - - - +
818M GLY 3.0 7.1 + - - +
819M VAL* 1.3 74.7 - - - +
821M GLU* 1.3 64.2 + - + +
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Residues in contact with GLU 821 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711M GLU* 3.5 1.7 - - - -
712M ALA* 2.5 47.3 + - + +
722M ILE* 3.0 35.5 - - - +
805M ARG* 3.7 13.7 + - + -
806M LEU 2.9 31.9 - - - +
807M ARG* 4.0 9.8 - - + +
808M ARG 5.2 0.7 - - - +
815M LEU* 3.8 4.9 - - - -
819M VAL* 3.4 2.7 - - - +
820M ARG* 1.3 91.5 + - + +
822M VAL* 1.3 60.9 + - - +
823M VAL* 3.0 28.0 - - - +
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Residues in contact with VAL 822 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709M GLU* 4.4 8.3 - - + +
710M ILE 3.6 5.4 - - - +
711M GLU* 3.3 32.8 - - + +
804M VAL 4.4 0.4 - - - +
805M ARG* 3.7 0.5 - - - -
806M LEU* 3.2 62.5 + - + -
815M LEU* 4.9 6.3 - - + -
816M LYS* 5.7 2.5 - - - +
819M VAL* 3.7 16.6 - - + -
821M GLU* 1.3 75.2 - - - +
823M VAL* 1.3 71.4 + - - +
824M ARG* 4.3 11.4 - - - +
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Residues in contact with VAL 823 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709M GLU* 3.7 3.0 - - - -
710M ILE* 2.6 49.9 + - + +
712M ALA 5.8 0.2 - - - +
722M ILE* 3.4 22.2 - - + -
742M VAL* 4.3 19.3 - - + -
756M VAL* 3.7 27.4 - - + -
804M VAL 3.2 9.9 - - - +
805M ARG* 4.8 4.3 - - + -
821M GLU* 3.0 26.7 - - - +
822M VAL* 1.3 76.3 - - - +
824M ARG* 1.3 65.6 + - - +
825M VAL* 4.0 1.4 + - + +
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Residues in contact with ARG 824 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84M ARG 5.6 0.4 + - - -
85M GLU* 2.9 31.9 + - - +
86M LYS* 4.3 7.9 - - - +
87M ASP* 4.5 16.8 + - - +
707M ARG* 3.2 43.1 - - + +
708M TYR 3.9 2.0 - - - -
709M GLU* 4.3 12.3 + - + +
803M THR* 3.3 6.5 - - - -
804M VAL* 2.8 61.0 + - + +
806M LEU* 4.3 20.0 - - - +
822M VAL* 4.3 10.2 - - - +
823M VAL* 1.3 70.7 - - - +
825M VAL* 1.3 69.0 + - - +
826M TYR* 3.6 30.3 - - + -
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Residues in contact with VAL 825 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708M TYR* 2.9 37.2 + - - +
742M VAL* 5.9 0.2 - - + -
743M VAL* 3.8 18.8 - - + -
755M LEU* 3.6 36.1 - - + +
756M VAL* 3.2 33.7 - - + -
790M LEU* 4.9 4.5 - - + -
800M VAL* 3.9 12.1 - - + -
802M ARG 3.8 2.0 - - - -
803M THR* 4.3 4.7 - - + -
823M VAL* 4.1 6.7 - - + +
824M ARG* 1.3 81.5 - - - +
826M TYR* 1.3 62.7 + - - +
827M VAL* 3.5 3.6 + - + -
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Residues in contact with TYR 826 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84M ARG 5.0 6.9 + - - -
85M GLU* 5.4 3.7 - - + -
630M ARG* 3.6 33.6 - - + +
705M ILE* 5.2 7.2 - - + -
706M GLU 3.6 4.9 - - - -
707M ARG* 3.1 44.1 + - + +
800M VAL* 3.6 4.7 - - - +
801M VAL* 3.0 41.4 + - + -
802M ARG* 2.9 43.9 + - + +
804M VAL* 4.6 2.2 - - + -
824M ARG* 3.6 31.5 - - + -
825M VAL* 1.3 73.6 - - - +
827M VAL* 1.3 62.0 + - - +
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Residues in contact with VAL 827 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704M HIS 3.8 0.2 - - - +
705M ILE* 3.5 4.9 - - - +
706M GLU* 3.0 31.3 + - - +
708M TYR* 3.7 25.6 - - + -
749M VAL* 3.5 8.7 - - + -
755M LEU* 3.6 30.7 - - + -
797M GLY* 4.2 1.6 - - - -
798M GLY 3.1 36.6 - - - +
799M ILE 3.2 12.8 - - - +
800M VAL* 4.4 3.6 - - + -
801M VAL* 4.9 0.4 - - - -
825M VAL* 3.8 4.7 - - + +
826M TYR* 1.3 81.6 - - - +
828M ALA* 1.3 62.8 + - - +
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Residues in contact with ALA 828 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65K PHE* 4.1 17.9 - - + -
703M ILE* 5.3 5.4 - - + -
704M HIS 3.4 7.4 - - - +
705M ILE* 3.6 21.5 - - + -
798M GLY* 3.0 2.2 - - - -
799M ILE* 2.7 36.3 + - - +
801M VAL* 3.8 18.8 - - + +
827M VAL* 1.3 74.8 - - - +
829M GLN* 1.3 62.0 + - - +
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Residues in contact with GLN 829 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65K PHE* 5.0 4.0 - - - -
154K GLU* 5.8 5.5 - - - +
702M SER 3.8 0.3 - - - +
703M ILE* 3.9 5.1 - - - -
704M HIS* 3.3 33.5 + - + +
750M LYS* 3.7 7.9 - - - +
796M GLU* 3.0 45.4 + - - +
797M GLY 3.2 16.9 + - - +
798M GLY* 3.6 11.2 - - - +
799M ILE* 5.1 3.6 - - + -
828M ALA* 1.3 79.9 - - - +
830M LYS* 1.3 72.8 + - - +
831M ARG* 3.6 25.5 + - + +
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Residues in contact with LYS 830 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64K GLU* 3.5 28.2 + - - +
65K PHE* 5.3 3.7 - - + -
76K VAL* 6.3 1.8 - - - -
79K ILE* 5.1 7.3 - - - +
83K LYS* 5.0 3.8 - - - +
153K ALA* 5.1 4.9 - - - +
154K GLU* 4.5 21.1 + - - +
167K VAL* 5.9 1.6 - - - +
168K ASP* 3.0 33.7 + - - -
572M ILE* 4.8 10.5 - - + -
698M ASP* 4.0 7.1 + - - +
701M THR* 3.5 31.2 - - + -
702M SER 4.1 6.1 - - - +
703M ILE* 5.1 7.6 - - + +
799M ILE* 5.8 1.4 - - - +
829M GLN* 1.3 81.6 - - - +
831M ARG* 1.3 60.3 + - - +
832M LYS* 3.6 18.8 + - + +
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Residues in contact with ARG 831 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700M TYR 3.7 1.2 - - - +
701M THR* 3.4 7.1 - - - -
702M SER* 3.0 40.3 + - - +
704M HIS* 3.1 49.5 + - + +
796M GLU* 5.7 5.1 - - - +
829M GLN* 4.3 26.2 + - + +
830M LYS* 1.3 70.7 - - - +
832M LYS* 1.3 63.1 + - - +
833M LEU 3.7 0.3 + - - -
837M ASP* 5.6 0.7 - - - +
996M LYS* 3.8 20.9 + - - +
999M HIS* 4.9 18.4 + - - +
1004M LYS* 3.1 40.6 - - - +
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Residues in contact with LYS 832 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K TYR* 2.9 28.1 + - - +
152K PRO* 3.9 16.5 - - + +
154K GLU* 3.3 22.1 + - - +
168K ASP* 2.8 36.4 + - - -
695M LEU* 4.5 17.3 - - + -
698M ASP* 4.6 8.3 - - - -
700M TYR 3.9 3.6 - - - -
701M THR* 4.3 10.3 - - + -
830M LYS* 3.6 17.9 + - + +
831M ARG* 1.3 73.8 - - - +
833M LEU* 1.3 67.5 + - - +
834M GLN* 3.0 14.0 + - - +
837M ASP* 4.9 1.2 - - - +
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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