Contacts of the helix formed by residues 555 - 565 (chain B) in PDB entry 2GRN
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 LEU 555 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502B PHE* 4.0 29.2 - - + -
509B SER* 3.8 30.5 - - - +
510B ASN* 3.8 22.2 - - - +
512B PHE* 5.0 2.9 - - + -
513B LEU* 3.9 27.8 - - + +
551B PHE* 3.8 15.7 - - + -
552B PRO* 2.9 23.9 + - + +
554B ALA* 1.3 80.5 - - + +
556B ALA* 1.3 65.3 + - - +
557B PRO 3.4 0.4 - - - -
558B LEU* 3.2 12.0 + - + +
559B LEU* 3.0 22.3 + - - +
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Residues in contact with ALA 556 (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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551B PHE* 4.0 13.8 - - + -
553B LYS 3.0 16.3 + - - +
555B LEU* 1.3 77.9 - - - +
557B PRO* 1.3 60.4 - - + +
559B LEU* 3.2 3.1 + - - +
560B LEU* 2.8 32.4 + - - +
584B LEU* 4.2 12.0 - - + +
587B VAL* 3.8 35.2 - - + -
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Residues in contact with PRO 557 (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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135A THR* 3.5 8.5 - - + +
139A GLN* 3.0 35.5 + - - +
553B LYS 3.4 6.3 - - - +
554B ALA* 3.4 17.5 - - - +
556B ALA* 1.3 95.5 - - + +
558B LEU* 1.3 60.3 + - + +
560B LEU* 3.4 6.6 + - + +
561B ALA* 2.9 23.9 + - - +
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Residues in contact with LEU 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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131A ALA* 4.5 16.2 - - + +
132A GLU* 4.8 18.2 - - + +
135A THR* 3.6 24.0 - - + +
510B ASN* 4.3 19.5 - - + +
513B LEU* 3.8 30.3 - - + -
514B THR* 6.1 0.2 - - - +
517B LEU* 4.6 0.2 - - - +
554B ALA 3.5 20.0 - - - +
555B LEU* 3.2 11.6 + - + +
557B PRO* 1.3 80.3 - - + +
559B LEU* 1.3 66.3 + - - +
561B ALA* 3.3 1.4 + - - +
562B PHE* 3.3 29.3 + - - +
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Residues in contact with LEU 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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513B LEU* 3.8 20.1 - - + +
516B LEU* 5.3 1.8 - - + -
517B LEU* 4.1 20.4 - - + -
520B MET* 6.0 0.7 - - + -
542B LEU* 4.0 38.8 - - + -
545B MET* 4.9 1.6 - - + -
546B VAL* 4.1 23.6 - - + -
551B PHE* 4.7 7.9 - - + -
555B LEU 3.0 12.2 + - - +
556B ALA* 3.6 8.1 - - - +
558B LEU* 1.3 75.6 - - - +
560B LEU* 1.3 63.6 + - - +
562B PHE* 3.2 3.4 + - - -
563B VAL* 3.0 44.3 + - + +
580B LEU* 5.1 1.8 - - + -
584B LEU* 4.3 13.2 - - + -
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Residues in contact with LEU 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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139A GLN* 4.6 11.0 - - - +
556B ALA 2.8 18.8 + - - +
557B PRO* 3.6 9.0 - - + +
559B LEU* 1.3 77.8 - - - +
561B ALA* 1.3 62.2 + - - +
564B THR* 3.0 37.2 + - + +
581B LEU* 3.3 28.3 - - + -
584B LEU* 3.8 31.1 - - + +
585B TYR* 3.9 28.5 - - + -
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Residues in contact with ALA 561 (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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134A TYR* 3.9 23.2 + - + -
135A THR* 3.5 24.2 - - + +
138A CYS* 5.8 2.2 - - + -
139A GLN* 3.9 11.6 - - + +
557B PRO 2.9 18.3 + - - +
558B LEU 3.6 3.1 - - - +
559B LEU 3.2 0.2 - - - -
560B LEU* 1.3 77.1 - - - +
562B PHE* 1.3 59.3 + - + +
564B THR* 3.2 16.4 + - - -
565B LYS* 3.3 15.9 + - - +
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Residues in contact with PHE 562 (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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128A PRO* 3.9 16.6 - - + -
131A ALA* 3.5 38.1 - - + -
134A TYR* 3.6 24.2 - + + -
135A THR* 4.2 2.0 - - - -
517B LEU* 3.6 34.5 - - + -
522B LEU* 3.5 35.7 - - + +
523B LEU* 3.7 26.0 - - + -
558B LEU 3.3 16.7 + - - +
559B LEU 3.2 3.7 + - - +
561B ALA* 1.3 77.4 - - + +
563B VAL* 1.3 63.2 + - - +
564B THR 3.4 0.7 - - - -
565B LYS* 3.9 22.6 + - + +
567B ASN* 5.8 0.2 - - - +
570B LEU* 3.6 13.2 - - - +
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Residues in contact with VAL 563 (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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520B MET* 6.1 0.7 - - + -
522B LEU* 4.9 7.4 - - + -
539B LEU* 4.7 11.4 - - + -
542B LEU* 5.6 0.7 - - + -
559B LEU* 3.0 32.8 + - + +
560B LEU* 4.8 0.2 - - - -
562B PHE* 1.3 78.4 - - - +
564B THR* 1.3 59.9 + - - +
565B LYS 3.3 0.2 - - - -
570B LEU* 3.3 8.1 - - + +
577B ARG* 2.7 48.2 + - + +
580B LEU* 3.9 30.1 - - + -
581B LEU* 3.6 29.2 - - + -
584B LEU* 4.8 1.3 - - + -
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Residues in contact with THR 564 (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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560B LEU* 3.0 27.8 + - + +
561B ALA* 3.2 9.2 + - - -
563B VAL* 1.3 78.4 - - - +
565B LYS* 1.3 64.9 + - - +
566B PRO* 3.4 6.1 - - - +
577B ARG* 3.3 8.6 + - - +
581B LEU* 3.2 33.2 - - + -
585B TYR* 5.2 4.9 - - + +
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Residues in contact with LYS 565 (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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125A ILE 4.1 3.6 - - - -
126A GLN* 3.0 29.1 + - - +
127A ASP* 4.9 1.2 + - - +
128A PRO* 3.6 23.0 - - - +
134A TYR* 3.3 32.3 - - + +
522B LEU 4.8 9.0 + - - +
561B ALA 3.3 13.7 + - - +
562B PHE* 4.0 23.6 - - + +
563B VAL 3.3 0.4 - - - -
564B THR* 1.3 80.5 + - - +
566B PRO* 1.3 88.9 + - + +
567B ASN* 3.3 3.3 + - + +
570B LEU* 3.7 10.9 - - - +
577B ARG* 3.1 11.0 + - - -
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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