Contacts of the helix formed by residues 678 - 691 (chain D) 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 ASN 678 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749A ASP 4.6 2.0 - - - -
635D SER* 3.6 29.5 - - - -
654D PHE* 3.8 7.7 - - - -
674D ASP 5.0 2.8 + - - +
675D ILE* 2.9 25.3 + - - +
677D ASP* 1.3 77.2 - - - +
679D GLY* 1.3 62.5 + - - +
680D ASP* 2.9 19.8 + - - +
681D ALA* 2.8 33.6 + - + +
682D ASN* 2.8 28.0 + - - -
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Residues in contact with GLY 679 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749A ASP 3.1 19.8 + - - -
750A LYS 3.4 21.5 - - - -
751A ILE 3.7 14.6 - - - -
752A PRO* 3.6 5.6 - - - +
753A ALA 5.3 0.4 - - - -
677D ASP 3.4 3.4 + - - -
678D ASN* 1.3 71.6 + - - +
680D ASP* 1.3 57.1 + - - +
682D ASN* 3.3 3.4 + - - -
683D TYR* 2.7 31.8 + - - +
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Residues in contact with ASP 680 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A LYS* 4.6 16.6 + - - -
749A ASP* 4.7 10.1 + - - +
751A ILE 5.5 0.7 - - - +
753A ALA 4.7 4.2 - - - +
654D PHE* 3.9 21.8 - - + +
655D ALA* 3.6 27.4 + - - +
678D ASN* 2.9 9.9 + - - +
679D GLY* 1.3 74.3 - - - +
681D ALA* 1.3 57.6 + - - +
683D TYR* 3.7 5.8 - - - +
684D TYR* 2.8 30.7 + - - +
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Residues in contact with ALA 681 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606D LEU* 4.2 6.7 - - + +
654D PHE* 3.9 27.9 - - + -
675D ILE* 3.8 22.0 - - + +
678D ASN* 2.8 22.5 + - + +
680D ASP* 1.3 69.5 - - - +
682D ASN* 1.3 67.8 + - - +
684D TYR* 3.3 19.5 - - - +
685D LEU* 3.5 12.5 + - - +
704D PHE* 4.7 9.2 - - + -
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Residues in contact with ASN 682 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750A LYS 5.5 1.4 + - - +
752A PRO* 4.0 12.3 - - + -
675D ILE 4.0 1.8 + - - -
676D ALA 3.0 27.6 + - - +
677D ASP* 4.1 2.2 - - - +
678D ASN 2.8 32.1 + - - +
679D GLY* 3.7 5.0 - - - +
681D ALA* 1.3 76.8 - - - +
683D TYR* 1.3 62.9 + - - +
685D LEU* 3.2 8.1 + - - +
686D MET* 3.1 21.9 + - - +
704D PHE* 3.5 16.1 - - - -
707D THR* 2.7 39.6 + - + +
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Residues in contact with TYR 683 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A LYS* 5.8 0.4 - - - -
683A TYR* 3.5 26.7 + + - -
752A PRO* 3.6 7.8 - - - +
753A ALA* 3.6 38.6 - - - +
309D LYS* 2.7 30.5 + - - -
313D ARG* 5.8 4.5 - - - -
679D GLY 2.7 20.6 + - - +
680D ASP* 3.9 6.5 - - - +
682D ASN* 1.3 70.4 - - - +
684D TYR* 1.3 66.6 + - - +
686D MET* 3.0 12.5 + - + -
687D GLU* 2.8 43.6 + - + +
753D ALA* 2.7 41.0 + - + -
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Residues in contact with TYR 684 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604D ALA* 3.2 16.0 - - + +
606D LEU* 4.0 17.3 - - + -
633D LEU* 3.2 25.0 - - + +
654D PHE* 3.6 27.1 - - + -
657D ALA 2.9 28.0 + - - -
658D PRO* 3.4 7.6 + - + -
659D SER* 3.3 34.5 + - - -
662D VAL* 4.0 4.7 - - - +
665D VAL* 3.7 24.5 - - + -
680D ASP 2.8 15.6 + - - +
681D ALA* 3.3 13.5 - - - +
683D TYR* 1.3 75.2 - - - +
685D LEU* 1.3 56.8 + - - +
687D GLU* 3.6 4.0 + - - -
688D ALA* 3.1 24.8 + - - +
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Residues in contact with LEU 685 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606D LEU* 4.1 5.8 - - + -
665D VAL* 3.8 29.6 - - + -
667D VAL* 4.1 13.0 - - + -
681D ALA 3.8 10.3 - - - +
682D ASN* 3.2 7.5 + - - +
683D TYR 3.2 0.4 - - - -
684D TYR* 1.3 78.6 - - - +
686D MET* 1.3 59.7 + - - +
688D ALA* 4.5 2.7 - - - -
689D TYR* 2.8 31.9 + - - +
695D ILE* 3.7 27.2 - - + +
697D LEU* 4.7 2.0 - - + -
704D PHE* 3.5 51.4 - - + +
707D THR* 5.5 2.7 - - + -
708D ILE* 4.0 14.1 - - + -
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Residues in contact with MET 686 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A MET* 4.8 2.9 - - + -
752A PRO* 3.5 45.3 - - + +
682D ASN 3.1 11.9 + - - +
683D TYR* 3.0 15.5 + - + +
685D LEU* 1.3 75.9 - - - +
687D GLU* 1.3 58.4 + - - +
689D TYR* 3.3 1.8 + - - +
690D LYS* 2.9 30.7 + - - +
707D THR* 3.8 32.3 - - + +
708D ILE* 4.0 9.0 - - + -
751D ILE* 4.1 17.2 - - + +
752D PRO* 3.3 31.0 - - + +
753D ALA* 4.1 10.3 - - + +
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Residues in contact with GLU 687 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D LYS* 2.7 35.7 + - - +
313D ARG* 5.4 1.4 + - - -
658D PRO* 3.9 6.4 - - - +
659D SER* 2.6 36.2 + - - +
660D LEU* 3.4 21.0 + - - +
683D TYR* 2.8 37.7 + - + +
684D TYR* 3.8 3.0 - - - +
686D MET* 1.3 71.7 - - - +
688D ALA* 1.3 65.7 + - - +
690D LYS* 3.3 6.7 + - + +
691D HIS* 3.0 46.6 + - + -
753D ALA* 4.7 2.9 - - - +
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Residues in contact with ALA 688 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659D SER* 3.3 12.7 + - - -
665D VAL* 3.7 27.4 - - + -
684D TYR 3.1 15.8 + - - +
685D LEU 3.9 3.4 - - - +
687D GLU* 1.3 78.8 - - - +
689D TYR* 1.3 61.5 + - - +
691D HIS* 3.4 5.1 + - - -
693D LYS* 3.0 43.3 + - + +
695D ILE* 4.4 9.0 - - + -
744D ARG* 3.7 0.3 + - - -
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Residues in contact with TYR 689 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685D LEU 2.8 19.9 + - - +
686D MET 3.6 3.6 - - - +
687D GLU 3.2 0.2 - - - -
688D ALA* 1.3 77.0 - - - +
690D LYS* 1.3 64.2 + - - +
692D LEU 3.0 4.3 + - - -
695D ILE* 3.9 4.2 - - + +
708D ILE* 3.7 40.5 + - + -
709D LYS 5.1 0.9 + - - -
710D ILE* 3.5 20.2 - - + +
715D GLU* 2.6 33.3 + - - -
718D ILE* 3.9 6.7 - - + -
744D ARG* 2.9 70.1 + - + +
747D LYS* 4.1 16.7 - - - +
748D ILE* 3.8 8.5 - - + +
751D ILE* 4.9 15.0 - - + -
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Residues in contact with LYS 690 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A ARG* 5.4 1.2 - - - +
680A ASP* 4.7 10.0 + - - -
303D VAL* 5.4 0.9 - - - +
305D ASP* 3.0 40.8 + - - +
309D LYS* 6.3 0.2 - - - +
686D MET 2.9 18.1 + - - +
687D GLU* 3.6 5.8 - - + +
689D TYR* 1.3 79.4 - - - +
691D HIS* 1.3 65.6 + - + +
692D LEU* 3.2 7.0 + - - +
748D ILE* 3.1 48.8 - - + +
751D ILE* 4.4 17.5 - - + -
753D ALA* 2.7 40.1 + - + +
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Residues in contact with HIS 691 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D VAL* 3.9 25.0 - - + +
305D ASP* 2.8 31.0 + - + -
306D GLU* 3.5 25.2 + - + +
309D LYS* 4.8 2.2 - - - -
659D SER* 4.7 2.2 + - - -
660D LEU* 3.5 27.6 - - + +
687D GLU* 3.0 33.0 + - + +
688D ALA 4.2 2.5 - - - +
689D TYR 3.2 0.4 - - - -
690D LYS* 1.3 87.4 - - + +
692D LEU* 1.3 69.8 + - - +
693D LYS* 3.2 13.6 + - + +
740D ARG* 3.0 27.5 + - - +
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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