Contacts of the helix formed by residues 624 - 643 (chain D) in PDB entry 6AH0
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 ARG 624 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619D LEU 4.3 2.9 - - - -
622D ASP* 3.0 2.2 - - - +
623D ASP* 1.3 76.1 - - - +
625D GLY* 1.3 65.4 + - - +
626D PRO 3.3 0.9 - - - -
627D VAL* 3.1 16.5 + - - -
628D LEU 4.0 2.4 + - - -
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Residues in contact with GLY 625 (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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619D LEU 3.3 17.1 + - - -
620D LEU* 3.5 18.1 - - - -
622D ASP 2.7 19.2 + - - -
623D ASP 3.0 1.4 - - - -
624D ARG* 1.3 78.5 - - - +
626D PRO* 1.3 61.3 - - - +
627D VAL 3.0 1.4 + - - -
628D LEU* 3.1 5.8 + - - -
629D GLU* 3.1 17.0 + - - -
892D GLN 5.7 2.0 - - - -
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Residues in contact with PRO 626 (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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623D ASP 4.2 4.8 - - - +
624D ARG 3.2 1.6 - - - -
625D GLY* 1.3 73.3 - - - +
627D VAL* 1.3 50.8 + - - +
629D GLU* 3.3 4.1 + - - +
630D ALA* 2.7 30.5 + - - -
892D GLN 5.3 3.0 - - - -
893D MET* 4.7 23.0 - - - +
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Residues in contact with VAL 627 (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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590D PRO 5.6 9.6 - - - +
591D GLU* 6.3 1.8 - - - +
624D ARG 3.1 8.6 + - - -
625D GLY 3.0 1.6 + - - -
626D PRO* 1.3 72.1 - - - +
628D LEU* 1.3 53.8 + - - +
629D GLU 3.0 0.9 - - - -
630D ALA* 2.8 5.4 + - - +
631D LEU* 2.8 32.1 + - - -
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Residues in contact with LEU 628 (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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590D PRO* 5.8 6.1 - - - +
624D ARG 4.0 3.6 + - - -
625D GLY* 3.1 7.1 + - - -
627D VAL* 1.3 73.5 - - - +
629D GLU* 1.3 59.6 + - - +
631D LEU* 3.9 2.0 - - - +
632D VAL* 3.1 21.7 + - - -
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Residues in contact with GLU 629 (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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625D GLY 3.1 11.8 + - - -
626D PRO* 3.5 6.1 - - - -
627D VAL 3.0 0.8 - - - -
628D LEU* 1.3 77.7 - - - +
630D ALA* 1.3 55.4 + - - +
632D VAL* 5.5 0.2 - - - +
633D ALA* 3.1 26.5 + - - -
923D ALA* 5.3 6.6 - - - -
924D TYR 5.6 7.4 - - - +
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Residues in contact with ALA 630 (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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626D PRO 2.7 16.4 + - - -
627D VAL* 2.8 5.4 + - - +
629D GLU* 1.3 74.4 - - - +
631D LEU* 1.3 66.0 + - - +
633D ALA* 5.2 0.2 - - - +
634D ARG* 3.1 17.0 + - - -
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Residues in contact with LEU 631 (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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594D ASP* 6.4 2.0 - - - +
627D VAL 2.8 16.7 + - - -
628D LEU* 3.9 2.9 - - - +
629D GLU 3.4 0.2 - - - -
630D ALA* 1.3 72.6 - - - +
632D VAL* 1.3 56.2 + - - +
634D ARG* 3.0 5.2 + - - -
635D ALA* 2.9 24.9 + - - -
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Residues in contact with VAL 632 (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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628D LEU 3.1 14.6 + - - -
631D LEU* 1.3 73.5 - - - +
633D ALA* 1.3 62.7 + - - +
635D ALA* 3.1 2.8 + - - +
636D ILE* 2.9 22.0 + - - -
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Residues in contact with ALA 633 (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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629D GLU 3.1 18.7 + - - -
630D ALA 4.1 0.4 - - - -
632D VAL* 1.3 73.7 - - - +
634D ARG* 1.3 57.5 + - - +
636D ILE* 3.8 1.0 - - - +
637D ARG* 2.9 29.1 + - - -
919D TRP 5.9 1.1 - - - -
922D TYR* 4.0 26.9 - - - +
923D ALA* 5.5 0.4 - - - +
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Residues in contact with ARG 634 (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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630D ALA 3.1 11.2 + - - -
631D LEU 3.0 7.7 + - - -
633D ALA* 1.3 74.1 - - - +
635D ALA* 1.3 57.4 + - - +
637D ARG* 3.8 0.8 - - - +
638D ASN* 2.9 29.1 + - - -
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Residues in contact with ALA 635 (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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631D LEU 2.9 13.4 + - - -
632D VAL* 3.1 4.7 + - - +
634D ARG* 1.3 75.4 - - - +
636D ILE* 1.3 61.1 + - - +
638D ASN* 3.4 1.3 + - - +
639D ILE* 3.0 19.4 + - - -
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Residues in contact with ILE 636 (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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632D VAL 2.9 15.5 + - - -
633D ALA* 3.8 1.3 - - - +
635D ALA* 1.3 72.7 - - - +
637D ARG* 1.3 64.8 + - - +
639D ILE* 2.9 14.1 + - - +
640D GLU* 3.2 9.5 + - - -
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Residues in contact with ARG 637 (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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633D ALA 2.9 20.2 + - - -
634D ARG* 3.8 0.9 - - - +
636D ILE* 1.3 70.8 - - - +
638D ASN* 1.3 60.1 + - - +
640D GLU* 3.6 8.4 + - - +
641D MET* 3.7 7.4 + - - -
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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 ARG 2.9 17.3 + - - -
635D ALA* 3.8 1.8 - - - +
637D ARG* 1.3 74.0 - - - +
639D ILE* 1.3 64.0 + - - +
640D GLU 3.2 1.8 - - - -
641D MET* 3.0 13.3 + - - +
642D THR* 3.1 11.4 + - - -
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Residues in contact with ILE 639 (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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635D ALA 3.0 11.6 + - - -
636D ILE* 2.9 7.7 + - - +
638D ASN* 1.3 75.9 - - - +
640D GLU* 1.3 57.2 + - - +
642D THR* 4.5 0.9 - - - +
643D GLN* 2.8 32.7 + - - -
644D GLU 4.1 16.5 - - - +
645D ASP* 5.7 1.3 - - - +
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Residues in contact with GLU 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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636D ILE 3.2 10.8 + - - -
637D ARG* 3.6 5.4 + - - +
638D ASN 3.2 1.2 - - - -
639D ILE* 1.3 78.0 - - - +
641D MET* 1.3 59.0 + - - +
643D GLN* 4.3 3.5 + - - -
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Residues in contact with MET 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 ARG 3.7 7.3 + - - -
638D ASN 3.0 7.7 + - - -
640D GLU* 1.3 79.1 - - - +
642D THR* 1.3 61.2 + - - +
643D GLN* 3.5 0.7 + - - -
1578D THR* 3.5 23.5 - - - +
1582D ALA* 5.4 12.1 + - - +
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Residues in contact with THR 642 (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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638D ASN 3.1 12.5 + - - -
639D ILE* 4.1 0.9 - - - +
641D MET* 1.3 76.2 - - - +
643D GLN* 1.3 57.3 + - - +
644D GLU* 2.9 14.1 + - - +
1578D THR* 6.1 1.3 - - - +
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Residues in contact with GLN 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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639D ILE 2.8 15.6 + - - -
640D GLU 4.3 3.3 + - - -
641D MET 3.3 3.8 + - - -
642D THR* 1.3 74.3 - - - +
644D GLU* 1.3 60.0 + - - +
645D ASP* 3.7 1.6 + - - -
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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