Contacts of the helix formed by residues 551 - 563 (chain A) in PDB entry 1GGE
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 ASP 551 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509A ARG* 2.8 26.7 + - + +
512A TRP* 3.1 35.7 + - + +
513A LEU* 4.6 2.4 - - - +
547A LEU 3.1 8.8 + - - +
548A ALA 4.4 0.6 + - - -
549A HIS 3.9 0.2 - - - -
550A ILE* 1.3 86.0 - - + +
552A LEU* 1.3 60.1 + - - +
553A THR* 3.0 14.4 + - - -
554A LEU* 2.9 31.1 + - + +
555A ALA* 2.9 24.3 + - - +
575A PRO* 5.8 1.3 - - - -
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Residues in contact with LEU 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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548A ALA* 3.1 35.2 - - + +
551A ASP* 1.3 75.3 + - - +
553A THR* 1.3 51.8 + - - +
555A ALA* 3.6 3.2 - - + +
556A GLN* 2.7 50.9 + - - +
566A LEU* 5.1 4.3 - - + -
570A GLN 3.7 16.2 - - - +
571A LEU* 3.1 33.7 - - + +
573A ILE 4.2 14.4 - - - +
575A PRO* 6.0 2.7 - - + -
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Residues in contact with THR 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A TRP* 4.6 11.0 - - + -
551A ASP* 3.0 13.2 + - - -
552A LEU* 1.3 76.5 - - - +
554A LEU* 1.3 59.6 + - - +
556A GLN* 3.8 8.1 - - - +
557A ALA* 2.9 31.5 + - + +
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Residues in contact with LEU 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A MET* 3.8 30.5 - - + -
512A TRP* 3.6 39.7 - - + -
523A ILE* 4.3 11.0 - - + -
524A VAL* 4.0 11.0 - - + -
527A PHE* 4.5 5.2 - - + -
547A LEU* 4.3 15.0 - - + -
550A ILE* 4.2 19.5 - - + -
551A ASP* 2.9 20.0 + - + +
553A THR* 1.3 76.7 - - - +
555A ALA* 1.3 63.5 + - - +
557A ALA* 3.2 4.7 + - - +
558A VAL* 3.2 37.8 + - + +
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Residues in contact with ALA 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A VAL* 4.2 6.7 - - - +
547A LEU* 3.7 14.1 - - + -
548A ALA* 3.5 42.0 - - + +
551A ASP 2.9 12.4 + - - +
552A LEU* 3.6 4.7 - - - +
554A LEU* 1.3 76.5 - - - +
556A GLN* 1.3 60.2 + - - +
558A VAL* 3.5 1.7 + - - +
559A ALA* 2.9 30.0 + - - +
566A LEU* 4.0 12.6 - - + -
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Residues in contact with GLN 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A LEU* 2.7 32.7 + - - +
553A THR* 3.9 7.7 - - - +
555A ALA* 1.3 74.7 - - - +
557A ALA* 1.3 56.8 + - - +
559A ALA* 3.8 3.8 - - + +
560A LYS* 3.0 30.5 + - - +
566A LEU* 3.4 22.6 - - + +
571A LEU* 3.4 27.1 - - - +
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Residues in contact with ALA 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A TRP* 6.1 0.2 - - + -
524A VAL* 3.7 31.0 - - + -
553A THR* 2.9 20.6 + - + +
554A LEU 3.9 0.2 - - - +
556A GLN* 1.3 75.4 - - - +
558A VAL* 1.3 64.5 + - - +
560A LYS* 3.5 6.9 + - - +
561A ASN* 3.4 24.8 + - - -
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Residues in contact with VAL 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A VAL* 4.1 14.1 - - - +
527A PHE* 3.9 25.4 - - + -
528A SER* 3.8 11.7 - - - +
531A LEU* 4.2 6.5 - - + -
544A VAL* 4.2 3.6 - - + -
547A LEU* 3.9 28.7 - - + -
554A LEU* 3.2 27.2 + - + +
555A ALA 3.9 2.7 - - - +
557A ALA* 1.3 74.3 - - - +
559A ALA* 1.3 65.6 + - - +
561A ASN* 3.1 5.9 + - - +
562A LEU* 3.1 38.9 + - + +
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Residues in contact with ALA 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A VAL* 4.0 12.7 - - + +
555A ALA 2.9 19.6 + - - +
556A GLN* 3.8 4.9 - - - +
558A VAL* 1.3 76.8 - - - +
560A LYS* 1.3 61.6 + - - +
562A LEU* 3.0 3.5 + - - +
563A GLY 2.9 4.3 + - - -
564A ILE* 2.8 51.3 + - + +
566A LEU* 3.9 22.9 - - + +
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Residues in contact with LYS 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A GLN 3.0 18.2 + - - +
557A ALA* 3.7 7.9 - - - +
558A VAL 3.3 0.2 - - - -
559A ALA* 1.3 74.7 - - - +
561A ASN* 1.3 68.1 + - - +
563A GLY* 3.1 12.1 + - - +
564A ILE 4.0 3.8 + - - -
636D ARG* 3.7 16.7 - - - +
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Residues in contact with ASN 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524A VAL* 3.7 14.3 - - - +
525A ASP* 4.3 8.3 + - - -
528A SER* 2.8 39.6 + - - +
557A ALA 3.4 13.0 + - - +
558A VAL 3.1 4.3 + - - +
560A LYS* 1.3 83.3 + - - +
562A LEU* 1.3 59.8 + - - +
563A GLY 3.3 0.9 - - - -
636D ARG* 3.3 13.1 - - + +
637D MET* 3.0 23.2 + - - +
653D THR* 5.4 0.7 - - - +
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Residues in contact with LEU 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A SER* 3.7 26.0 - - - +
531A LEU* 3.8 33.0 - - + -
532A SER* 4.0 13.0 - - - +
540A ARG* 4.2 14.6 + - + -
544A VAL* 3.9 19.5 - - + -
558A VAL* 3.1 14.7 + - + +
559A ALA 3.0 6.8 + - - +
561A ASN* 1.3 81.8 - - - +
563A GLY* 1.3 62.7 + - - +
564A ILE* 3.2 24.0 + - + +
637D MET* 3.5 32.7 - - + +
638D GLY* 3.5 6.1 + - - -
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Residues in contact with GLY 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A ALA 2.9 3.5 + - - -
560A LYS* 3.1 12.0 + - - -
561A ASN 3.3 0.8 - - - -
562A LEU* 1.3 80.8 - - - +
564A ILE* 1.3 59.9 + - - +
565A GLU 4.3 0.2 + - - -
636D ARG* 4.2 11.9 - - - -
637D MET 3.5 13.5 + - - -
638D GLY* 4.3 6.7 - - - -
639D GLU 5.3 0.7 + - - -
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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