Contacts of the strand formed by residues 555 - 560 (chain B) in PDB entry 2P1N
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 ARG 555 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LEU* 2.8 31.8 + - - +
86B PRO* 3.8 14.0 - - - +
512B TRP* 3.8 21.5 - - + -
513B MET 3.3 9.2 - - - +
514B SER* 3.8 11.4 - - - -
537B VAL* 3.6 7.1 - - - +
538B ILE* 2.8 68.2 + - + +
539B ASP* 4.1 1.0 - - - +
540B GLU* 3.8 19.2 + - - +
553B VAL* 3.4 4.8 - - - -
554B GLU* 1.3 111.0 + - - +
556B VAL* 1.3 56.7 + - - +
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Residues in contact with VAL 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B LEU* 5.9 0.9 - - + -
511B LEU 3.8 2.1 - - - +
512B TRP* 3.8 2.5 - - - -
513B MET* 2.9 56.5 + - + +
518B VAL* 4.3 24.9 - - + -
523B CYS* 3.2 30.3 - - - -
535B VAL* 4.0 19.1 - - + -
536B GLU 3.2 13.2 - - - +
537B VAL* 4.5 0.7 - - + -
553B VAL* 4.1 3.3 - - + +
555B ARG* 1.3 74.4 - - - +
557B PHE* 1.3 57.5 + - - +
558B ILE* 4.2 15.4 - - + +
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Residues in contact with PHE 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASN* 5.6 5.6 - - - -
77B PRO* 3.2 36.1 - - + -
89B TRP* 3.7 29.8 - + - -
510B SER* 3.6 33.4 - - - -
511B LEU 3.6 9.2 - - - -
512B TRP* 3.5 20.4 - + + -
534B ASN 3.8 2.3 - - - +
536B GLU* 2.8 36.9 + - + +
538B ILE* 3.8 19.2 - - + +
555B ARG 4.3 0.2 - - - -
556B VAL* 1.3 73.5 - - - +
558B ILE* 1.3 61.8 + - - +
559B TYR* 3.4 31.1 - + + -
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Residues in contact with ILE 558 (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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498B LEU* 4.0 22.0 - - + -
505B LEU* 4.1 22.2 - - + -
510B SER* 3.1 5.8 - - - -
511B LEU* 2.7 53.3 + - + +
526B LEU* 3.4 24.9 - - + -
533B LEU* 4.1 22.4 - - + -
534B ASN 3.5 3.6 - - - +
535B VAL* 3.8 23.1 - - + -
556B VAL* 4.2 16.2 - - + -
557B PHE* 1.3 77.3 - - - +
559B TYR* 1.3 65.5 + - - +
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Residues in contact with TYR 559 (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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52B ASN* 3.4 19.1 - - - +
54B TYR* 3.5 28.3 - + + +
89B TRP* 5.0 3.4 - + - -
509B ARG 3.4 16.8 - - - +
510B SER* 4.2 7.2 - - - +
533B LEU* 3.7 4.8 - - - -
534B ASN* 2.9 59.2 + - + -
536B GLU* 2.6 37.3 + - + -
557B PHE* 3.4 34.1 - + + -
558B ILE* 1.3 77.2 - - - +
560B ARG* 1.3 66.2 + - - +
561B THR* 4.3 1.6 - - + -
566B ARG* 3.4 14.7 - - - -
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Residues in contact with ARG 560 (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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156A GLN* 3.6 26.7 + - - +
157A TRP* 3.4 53.8 + - + +
160A GLU* 5.7 0.6 + - - -
52B ASN* 4.4 0.7 - - - +
55B ALA* 4.1 11.5 - - + +
505B LEU 4.4 6.3 + - - +
506B GLU* 2.7 36.5 + - - -
507B THR* 3.2 18.6 + - - +
508B MET 3.1 27.6 + - - +
509B ARG* 3.7 13.9 + - - +
532B LYS 3.5 7.0 - - - -
533B LEU* 3.8 15.4 - - + +
559B TYR* 1.3 78.6 - - - +
561B THR* 1.3 64.4 + - - +
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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