Contacts of the helix formed by residues 629 - 639 (chain A) in PDB entry 6A5T
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 GLY 629 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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589A LEU* 5.2 3.4 - - - -
621A LYS 4.6 4.7 - - - -
622A THR* 3.1 17.3 - - - -
624A GLY 5.3 1.3 - - - -
626A GLY* 3.0 20.6 + - - -
627A GLY 3.0 2.1 + - - -
628A GLY* 1.3 77.3 - - - +
630A LEU* 1.3 67.7 + - - +
631A ILE 3.4 2.2 - - - -
632A HIS* 3.6 4.2 + - - +
633A THR* 2.8 22.5 + - - -
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Residues in contact with LEU 630 (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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583A ILE* 4.0 36.6 - - + -
587A ILE* 4.3 15.9 - - + -
589A LEU* 4.7 15.2 - - + +
608A ILE* 5.1 7.9 - - + -
622A THR* 2.4 37.6 + - + +
623A VAL* 4.1 22.7 - - + -
629A GLY 1.3 67.1 - - - -
631A ILE* 1.3 57.1 + - + +
633A THR* 2.6 29.9 + - - -
634A VAL* 3.0 31.6 + - + -
646A LEU* 4.7 12.6 - - + -
650A ILE* 5.4 2.0 - - + -
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Residues in contact with ILE 631 (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 ILE* 4.4 11.4 - - + -
520A PRO* 4.8 9.0 - - + -
522A MET 4.0 7.6 - - - +
523A GLY* 4.1 7.0 - - - +
524A ILE* 4.3 5.6 - - + -
622A THR 4.4 0.6 + - - -
623A VAL* 3.2 30.9 - - + +
624A GLY 4.4 4.2 + - - +
629A GLY 3.4 0.8 - - - -
630A LEU* 1.3 78.1 - - + +
632A HIS* 1.3 64.7 + - - +
634A VAL* 3.3 2.2 + - - +
635A MET* 2.9 22.2 + - - +
643A CYS* 3.6 24.2 - - - -
646A LEU* 4.1 20.9 - - + -
647A PHE* 3.6 36.3 - - + -
650A ILE* 5.8 0.7 - - + -
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Residues in contact with HIS 632 (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 ILE* 6.4 0.2 - - - -
513A VAL* 4.6 18.5 - - + +
518A ASN 4.0 19.6 + - - -
520A PRO* 3.5 28.7 - - + +
628A GLY* 3.2 30.3 + - - +
629A GLY 3.6 10.9 + - - +
630A LEU 3.2 0.4 - - - -
631A ILE* 1.3 78.2 - - - +
633A THR* 1.3 65.0 + - - +
635A MET* 3.1 5.2 + - - +
636A ARG* 3.0 46.9 + - + +
879A VAL 4.2 15.8 + - - -
880A GLU* 4.3 15.5 - - + -
964A ARG* 5.8 1.3 + - - -
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Residues in contact with THR 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A ILE* 4.7 4.7 - - + -
588A HIS 4.1 19.3 - - - +
589A LEU* 4.8 8.0 - - + +
628A GLY* 4.0 8.7 + - - -
629A GLY 2.8 15.6 + - - -
630A LEU* 2.6 22.0 + - - -
632A HIS* 1.3 76.7 - - - +
634A VAL* 1.3 62.9 + - - +
636A ARG* 3.3 5.0 + - - +
637A GLU* 2.9 31.3 + - + +
964A ARG* 3.6 36.0 + - - +
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Residues in contact with VAL 634 (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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583A ILE* 4.9 5.2 - - + -
584A PRO* 4.1 25.6 - - + -
587A ILE* 3.8 24.7 - - + -
630A LEU* 3.0 36.2 + - + +
631A ILE* 4.0 7.0 - - - +
633A THR* 1.3 76.4 - - - +
635A MET* 1.3 64.8 + - - +
637A GLU* 3.1 5.5 + - - -
638A LYS* 2.9 30.5 + - + +
639A GLY 4.4 0.3 - - - +
642A ILE* 4.7 6.5 - - + +
643A CYS* 5.0 10.5 - - - -
646A LEU* 5.2 10.1 - - + -
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Residues in contact with MET 635 (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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509A PRO 4.1 7.6 - - - +
510A LEU* 5.4 4.7 - - + -
512A ILE* 3.6 14.4 - - + -
513A VAL* 4.1 24.7 - - + -
631A ILE 2.9 13.8 + - - +
632A HIS* 3.3 12.1 - - - +
634A VAL* 1.3 75.6 - - - +
636A ARG* 1.3 68.2 + - - +
637A GLU 2.9 0.3 + - - -
639A GLY* 2.9 51.9 + - - +
640A PRO* 3.4 38.4 - - + -
643A CYS* 3.6 19.4 - - - -
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Residues in contact with ARG 636 (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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513A VAL* 5.6 3.8 - - - -
632A HIS* 3.0 43.4 + - + +
633A THR* 3.7 7.2 - - - +
635A MET* 1.3 81.0 - - - +
637A GLU* 1.3 59.9 + - - +
638A LYS 3.6 0.2 + - - -
639A GLY 4.5 2.1 + - - -
877A THR 5.3 4.3 - - - -
878A GLN* 2.3 56.7 + - - +
879A VAL 5.6 0.4 - - - -
880A GLU* 4.2 15.6 + - - +
960A VAL* 5.3 10.3 - - - +
961A ASN 5.9 0.2 - - - +
964A ARG* 4.3 15.8 - - - +
1054A GLN* 4.4 29.0 + - - +
1058A SER* 5.8 1.0 - - - -
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Residues in contact with GLU 637 (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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586A GLY 4.5 7.5 - - - +
587A ILE* 4.4 17.0 - - + -
588A HIS 6.1 0.4 - - - +
633A THR* 2.9 24.2 + - + +
634A VAL* 3.8 6.3 - - - +
635A MET 3.0 0.2 - - - -
636A ARG* 1.3 79.6 - - + +
638A LYS* 1.3 72.9 + - + +
639A GLY 3.9 0.2 - - - -
964A ARG* 2.9 36.8 + - - +
965A ILE* 5.3 4.3 + - - +
968A ASN* 3.2 27.2 + - - -
1054A GLN* 6.0 0.3 + - - -
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Residues in contact with LYS 638 (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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584A PRO* 5.1 8.1 - - + -
585A SER 3.8 22.8 + - - -
586A GLY* 4.8 10.9 - - - -
587A ILE* 5.1 4.3 - - + -
634A VAL* 2.9 21.3 + - + +
637A GLU* 1.3 90.2 - - + +
639A GLY* 1.3 61.4 + - - +
640A PRO* 4.6 0.7 - - - +
641A LYS* 5.2 0.3 + - - +
642A ILE* 3.7 42.2 + - + +
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Residues in contact with GLY 639 (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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635A MET* 2.9 32.3 + - - +
636A ARG 4.5 2.0 + - - -
637A GLU 3.9 0.4 - - - -
638A LYS* 1.3 82.5 - - - +
640A PRO* 1.3 76.1 - - - +
643A CYS* 3.7 8.0 + - - +
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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