Contacts of the helix formed by residues 630 - 643 (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 LYS 630 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569C ASN* 3.6 33.8 - - - +
625D GLU 3.6 3.8 + - - +
626D PHE* 3.0 37.4 + - + +
629D GLY* 1.3 83.2 - - - +
631D HIS* 1.3 70.1 + - - +
632D LEU 3.4 0.9 - - - -
633D LYS* 3.4 2.6 + - - +
634D THR* 3.0 29.7 + - - +
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Residues in contact with HIS 631 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560C GLU* 3.7 10.1 - - - -
564C TYR* 2.7 33.3 + + - -
569C ASN* 3.3 29.2 - - + +
626D PHE 2.9 26.9 + - - -
627D HIS* 3.3 18.8 - - + +
630D LYS* 1.3 77.8 - - - +
632D LEU* 1.3 59.1 + - - +
634D THR* 3.2 5.9 + - - -
635D TYR* 3.0 47.7 + - + -
761D HIS* 3.4 34.7 + + + +
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Residues in contact with LEU 632 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605D LEU* 3.5 20.2 - - + -
606D ILE* 4.1 4.7 - - + +
627D HIS 3.1 13.2 + - - +
628D HIS* 3.4 19.3 + - + +
630D LYS 3.4 0.2 - - - -
631D HIS* 1.3 71.5 - - - +
633D LYS* 1.3 68.2 + - - +
635D TYR* 3.0 9.1 + - + -
636D VAL* 2.9 30.8 + - + +
670D GLN 4.3 0.7 - - - +
671D THR* 4.0 22.7 - - - +
674D HIS* 3.6 36.8 - - + +
675D ASN* 4.0 14.8 - - - +
678D PHE* 3.8 19.7 - - + -
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Residues in contact with LYS 633 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605D LEU* 3.7 25.7 - - + +
628D HIS 3.7 4.0 + - - -
629D GLY 3.3 23.6 - - - +
630D LYS* 3.4 4.0 + - - +
631D HIS 3.3 0.4 - - - -
632D LEU* 1.3 78.9 - - - +
634D THR* 1.3 61.3 + - - +
636D VAL* 3.3 3.7 + - + +
637D ASP* 2.8 71.5 + - - +
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Residues in contact with THR 634 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569C ASN* 5.1 4.3 + - - -
630D LYS 3.0 15.3 + - - -
631D HIS* 3.4 10.5 - - - -
632D LEU 3.1 0.2 - - - -
633D LYS* 1.3 79.2 - - - +
635D TYR* 1.3 69.5 + - + +
637D ASP* 3.8 6.1 - - - +
638D ASN* 3.0 42.2 + - - +
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Residues in contact with TYR 635 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519C PHE* 3.9 14.1 - + - -
631D HIS* 3.0 39.8 + - + -
632D LEU* 3.0 11.0 + - + +
634D THR* 1.3 80.1 - - + +
636D VAL* 1.3 57.2 + - - +
638D ASN* 5.2 1.6 - - - -
639D LEU* 2.9 29.6 + - - +
667D ASN* 3.4 23.5 - - - +
670D GLN* 3.0 46.1 + - + -
671D THR* 3.9 13.2 + - - +
674D HIS* 3.4 31.6 - + - -
759D TRP* 3.6 20.3 - - - -
761D HIS* 3.9 8.5 - + - -
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Residues in contact with VAL 636 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603D HIS* 3.1 35.9 - - + +
604D GLU* 3.9 22.2 - - - +
605D LEU* 4.2 8.7 - - + +
632D LEU* 2.9 26.8 + - + +
633D LYS* 3.7 6.3 - - + +
635D TYR* 1.3 78.3 - - - +
637D ASP* 1.3 65.9 + - - +
639D LEU* 3.2 5.1 + - - +
640D ASN* 3.0 26.6 + - - +
671D THR* 3.9 25.8 - - + +
675D ASN* 5.8 0.4 - - - +
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Residues in contact with ASP 637 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633D LYS* 2.8 55.8 + - - +
634D THR* 3.8 5.8 - - - +
636D VAL* 1.3 81.5 - - - +
638D ASN* 1.3 66.2 + - - +
640D ASN* 3.4 10.8 + - - +
641D LYS* 3.1 23.7 + - - +
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Residues in contact with ASN 638 (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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634D THR* 3.0 34.8 + - - +
635D TYR* 5.2 1.2 - - - -
637D ASP* 1.3 77.3 - - - +
639D LEU* 1.3 60.9 + - - +
641D LYS* 3.2 9.4 + - - +
642D LEU* 2.8 41.6 + - + +
667D ASN* 3.2 35.6 + - - +
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Residues in contact with LEU 639 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603D HIS* 3.9 31.4 - - + +
635D TYR 2.9 17.4 + - - +
636D VAL* 3.5 4.5 - - - +
638D ASN* 1.3 75.7 - - - +
640D ASN* 1.3 64.1 + - - +
642D LEU* 3.4 2.4 + - - -
643D ILE* 3.2 49.5 + - + +
653D LEU* 3.9 22.9 - - + -
656D ILE* 4.3 7.4 - - + -
664D ILE* 4.1 6.7 - - + +
667D ASN* 3.8 8.9 - - + +
668D ALA* 3.8 26.7 - - + +
671D THR* 3.8 19.5 - - + +
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Residues in contact with ASN 640 (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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601D MET 3.6 18.2 + - - +
602D THR* 4.0 7.1 - - - +
603D HIS* 2.8 59.8 + - - +
636D VAL* 3.0 22.2 + - - +
637D ASP* 3.6 9.8 + - - +
639D LEU* 1.3 79.8 - - - +
641D LYS* 1.3 60.1 + - - +
643D ILE* 3.7 9.5 - - - +
644D ILE* 3.4 23.2 - - - +
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Residues in contact with LYS 641 (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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637D ASP 3.1 16.9 + - - +
638D ASN* 3.6 11.0 - - - +
639D LEU 3.2 0.2 - - - -
640D ASN* 1.3 79.7 - - - +
642D LEU* 1.3 72.6 + - + +
643D ILE 3.6 0.5 + - - -
644D ILE* 3.7 20.4 + - - +
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Residues in contact with LEU 642 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638D ASN* 2.8 24.7 + - + +
639D LEU* 3.4 2.2 + - - +
641D LYS* 1.3 83.5 - - + +
643D ILE* 1.3 61.6 + - - +
644D ILE 3.3 6.5 + - - +
646D THR* 3.9 3.8 - - - +
663D GLY* 3.7 21.1 - - - +
664D ILE* 3.6 27.5 - - + +
667D ASN* 3.4 30.1 - - + +
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Residues in contact with ILE 643 (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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601D MET* 3.5 19.5 - - + +
603D HIS* 5.3 6.7 - - + +
639D LEU* 3.2 40.3 + - + +
640D ASN* 3.7 7.0 - - - +
642D LEU* 1.3 75.1 - - - +
644D ILE* 1.3 73.4 + - + +
646D THR* 2.8 27.6 + - - -
648D PHE* 3.9 21.8 - - + +
649D GLU* 3.2 40.9 - - + +
656D ILE* 4.2 4.7 - - + -
664D ILE* 3.8 20.9 - - + -
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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
------------------------------------------------------------
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