Contacts of the helix formed by residues 661 - 680 (chain D) in PDB entry 1UES
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 GLU 661 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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648D PHE* 5.0 1.0 - - - -
659D LYS 4.5 5.1 - - - +
660D SER* 1.3 75.5 - - - +
662D GLY* 1.3 71.6 + - - +
663D GLY 3.6 0.2 + - - -
664D ILE* 3.4 10.0 + - - +
665D PHE* 3.1 15.1 + - - +
747D ARG* 2.9 26.5 + - - -
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Residues in contact with GLY 662 (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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661D GLU* 1.3 78.4 + - - +
663D GLY* 1.3 58.4 - - - -
665D PHE* 3.0 3.9 + - - +
666D ASN* 2.9 36.0 + - - +
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Residues in contact with GLY 663 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642D LEU* 3.8 15.9 - - - -
662D GLY* 1.3 70.5 - - - -
664D ILE* 1.3 62.7 + - - +
666D ASN* 3.3 11.5 + - - +
667D ASN* 3.0 30.8 + - - -
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Residues in contact with ILE 664 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639D LEU* 4.1 4.4 - - + +
642D LEU* 3.6 41.2 - - + +
643D ILE* 3.8 13.9 - - + -
646D THR* 3.8 28.9 - - + +
648D PHE* 4.2 9.9 - - + -
656D ILE* 3.4 28.7 - - + -
660D SER* 3.6 9.6 - - - -
661D GLU 3.4 8.2 + - - +
662D GLY 3.2 0.8 - - - -
663D GLY* 1.3 75.8 - - - +
665D PHE* 1.3 59.6 + - - +
667D ASN* 3.3 1.2 + - - -
668D ALA* 2.8 27.2 + - - +
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Residues in contact with PHE 665 (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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657D VAL* 3.1 41.7 - - + -
660D SER* 3.1 28.2 + - - +
661D GLU* 3.1 10.9 + - - -
662D GLY 3.0 8.7 + - - +
664D ILE* 1.3 79.3 - - - +
666D ASN* 1.3 67.2 + - - +
668D ALA* 4.4 1.6 - - - -
669D GLY* 2.7 31.4 + - - -
742D ALA* 3.6 34.5 - - + -
743D GLY* 4.0 11.9 - - - -
744D ASN 4.5 3.1 - - - -
747D ARG* 3.5 31.0 - - - -
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Residues in contact with ASN 666 (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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519C PHE* 3.4 54.6 - - + +
662D GLY* 2.9 23.9 + - - +
663D GLY* 3.6 12.3 - - - +
664D ILE 3.3 0.2 - - - -
665D PHE* 1.3 86.8 - - - +
667D ASN* 1.3 59.3 + - - +
670D GLN* 3.1 31.5 + - - +
741D ASN* 5.5 0.9 - - - +
742D ALA* 3.2 8.5 + - - +
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Residues in contact with ASN 667 (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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519C PHE* 5.1 2.9 - - - -
635D TYR* 3.4 33.3 - - - +
638D ASN* 3.2 32.8 + - - +
639D LEU* 3.8 15.3 - - - +
642D LEU* 3.4 18.6 - - - +
663D GLY* 3.0 26.6 + - - +
664D ILE 4.2 0.9 - - - +
666D ASN* 1.3 78.4 - - - +
668D ALA* 1.3 61.6 + - - +
670D GLN* 3.8 4.4 - - - +
671D THR* 2.8 33.9 + - - -
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Residues in contact with ALA 668 (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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639D LEU* 3.8 17.8 - - + +
653D LEU* 3.7 4.5 - - + +
656D ILE* 3.6 29.2 - - + -
657D VAL* 3.4 21.2 - - + +
664D ILE 2.8 18.4 + - - +
665D PHE* 3.9 4.0 - - - +
667D ASN* 1.3 74.2 - - - +
669D GLY* 1.3 61.6 + - - +
671D THR* 3.1 2.4 + - - -
672D LEU 2.9 26.5 + - - -
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Residues in contact with GLY 669 (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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657D VAL* 3.8 18.6 - - - +
665D PHE* 2.7 21.8 + - - -
668D ALA* 1.3 73.5 - - - +
670D GLN* 1.3 55.7 + - - +
672D LEU* 3.5 1.0 + - - +
673D ASN* 2.8 35.4 + - - -
742D ALA* 3.4 23.3 - - - -
744D ASN* 4.9 0.4 - - - +
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Residues in contact with GLN 670 (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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519C PHE* 3.4 19.7 - - + -
635D TYR* 3.0 51.9 + - + -
666D ASN 3.1 22.9 + - - +
667D ASN 3.9 1.1 - - - +
669D GLY* 1.3 75.0 - - - +
671D THR* 1.3 63.3 + - - +
673D ASN* 3.6 1.1 + - - -
674D HIS* 2.6 44.9 + - - -
723D TRP* 2.9 26.6 + - - -
742D ALA* 3.4 11.1 - - + +
759D TRP* 3.4 23.6 - - - +
761D HIS* 4.9 0.2 - - - -
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Residues in contact with THR 671 (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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603D HIS* 5.6 4.3 - - + -
604D GLU 5.2 2.9 - - - +
632D LEU* 4.0 7.9 - - + -
635D TYR 3.9 16.1 + - - -
636D VAL* 3.9 20.0 - - + +
639D LEU* 3.8 17.4 - - + +
653D LEU* 4.0 12.6 - - + -
667D ASN 2.8 22.3 + - - -
668D ALA 3.1 4.2 + - - -
670D GLN* 1.3 78.2 - - - +
672D LEU* 1.3 65.0 + - - +
674D HIS* 3.9 0.9 - - - +
675D ASN* 2.9 46.7 + - - +
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Residues in contact with LEU 672 (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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653D LEU* 3.8 19.7 - - + +
654D ASN* 3.6 26.7 - - - +
657D VAL* 3.9 20.9 - - + -
668D ALA 2.9 14.9 + - - +
669D GLY 4.0 1.8 - - - +
671D THR* 1.3 76.6 - - - +
673D ASN* 1.3 63.6 + - - +
675D ASN* 3.3 6.3 + - + +
676D LEU* 3.1 42.0 + - + +
744D ASN* 3.5 33.2 - - - +
746D VAL* 4.3 9.4 - - + -
752D PRO* 5.2 0.9 - - + -
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Residues in contact with ASN 673 (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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669D GLY 2.8 27.7 + - - +
670D GLN* 3.6 3.5 + - - +
672D LEU* 1.3 73.1 - - - +
674D HIS* 1.3 58.4 + - - +
676D LEU* 3.8 2.1 - - - +
677D TYR* 2.9 28.9 + - - +
723D TRP* 3.3 46.5 - - + +
725D TRP* 3.0 22.7 + - - -
742D ALA 3.2 9.7 + - - -
743D GLY 2.9 21.7 + - - +
744D ASN* 2.8 24.5 - - - +
755D THR* 4.2 2.4 - - - +
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Residues in contact with HIS 674 (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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627D HIS* 3.2 19.1 + + - -
632D LEU* 3.6 29.6 - - + -
635D TYR* 3.4 29.1 - + - -
670D GLN* 2.6 34.9 + - - +
673D ASN* 1.3 74.4 - - - +
675D ASN* 1.3 67.7 + - - +
677D TYR* 3.9 5.6 - + - -
678D PHE* 2.8 41.6 + + + -
723D TRP* 3.3 22.6 - + - -
761D HIS* 4.0 0.6 + - - -
792D MN 2.2 35.7 + - - -
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Residues in contact with ASN 675 (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 GLU 5.1 5.2 + - - +
606D ILE* 3.5 39.7 + - + +
632D LEU* 4.0 8.3 - - - +
636D VAL* 5.8 0.2 - - - +
653D LEU* 3.9 13.7 - - - +
671D THR* 2.9 38.7 + - - +
672D LEU* 3.6 8.1 - - + +
674D HIS* 1.3 76.7 - - - +
676D LEU* 1.3 61.8 + - + +
678D PHE* 4.4 0.2 - - - -
679D THR* 2.9 31.2 + - - +
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Residues in contact with LEU 676 (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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672D LEU* 3.1 42.3 + - + +
673D ASN 3.9 0.4 - - - +
675D ASN* 1.3 74.7 - - + +
677D TYR* 1.3 67.2 + - - +
679D THR* 3.7 0.9 - - - +
680D GLN* 3.3 12.8 + - - +
725D TRP* 3.6 32.5 - - + -
744D ASN* 4.4 0.2 - - - +
752D PRO* 3.9 20.6 - - + +
790D ARG* 2.8 50.5 + - + +
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Residues in contact with TYR 677 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619D ILE* 3.5 19.0 - - + +
627D HIS* 3.6 28.5 + + - -
673D ASN 2.9 18.9 + - - +
674D HIS* 3.5 7.0 - + - +
676D LEU* 1.3 76.5 - - - +
678D PHE* 1.3 90.3 + + - +
680D GLN* 3.2 17.8 - - - +
681D PHE* 3.2 45.6 - + - -
723D TRP* 4.0 11.2 - + + -
755D THR* 3.6 22.1 - - + +
756D PHE* 4.3 1.8 - - - -
757D ASP* 3.5 30.5 - - + +
762D ALA* 4.0 12.1 + - - +
774D HIS* 4.3 8.3 + - - -
778D LEU* 4.8 3.0 - - + +
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Residues in contact with PHE 678 (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 ILE* 5.0 3.8 - - + -
608D LEU* 3.6 22.2 - - + -
609D PRO* 5.0 0.2 - - - -
610D TYR* 2.7 39.4 + - - -
615D LEU* 5.5 2.9 - - + -
619D ILE* 5.7 4.5 - - + -
624D VAL* 5.3 9.9 - - + -
627D HIS* 3.6 24.7 - + + -
628D HIS* 3.6 44.6 - + + -
632D LEU* 3.8 22.0 - - + -
674D HIS* 2.8 40.1 + + - +
675D ASN 4.5 1.3 - - - +
677D TYR* 1.3 94.7 - + - +
679D THR* 1.3 63.8 + - + +
680D GLN 3.4 0.5 + - - -
681D PHE* 3.7 6.8 + + - +
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Residues in contact with THR 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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606D ILE* 3.2 27.8 - - + -
607D SER 5.2 0.4 - - - +
609D PRO* 4.3 20.6 - - + -
675D ASN 2.9 20.8 + - - +
676D LEU* 3.7 2.3 - - - +
677D TYR 3.2 0.4 - - - -
678D PHE* 1.3 78.1 - - + +
680D GLN* 1.3 57.3 - - - +
681D PHE 3.4 0.7 - - - -
682D ARG* 3.1 19.9 + - - -
786D ILE* 3.7 13.7 - - - +
790D ARG* 3.0 20.1 + - - -
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Residues in contact with GLN 680 (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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676D LEU 3.3 11.3 + - - +
677D TYR* 3.2 19.5 + - - +
679D THR* 1.3 77.1 - - - +
681D PHE* 1.3 85.4 + - + +
682D ARG* 4.6 0.2 - - - -
754D LEU* 3.6 16.6 - - + +
755D THR* 2.6 42.3 + - - +
782D VAL* 3.9 1.5 - - + +
783D ASP* 2.9 33.2 + - - +
786D ILE* 4.1 6.5 - - - -
787D VAL* 4.3 10.8 - - + -
790D ARG* 3.1 30.4 + - - +
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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