Contacts of the helix formed by residues 630 - 640 (chain D) in PDB entry 4Z2C
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 VAL 630 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A GLY* 4.1 26.5 - - - +
628D ASP 3.5 7.8 + - - +
629D ARG* 1.3 75.4 - - - +
631D GLU* 1.3 71.5 + - + +
632D PRO 3.4 0.2 - - - -
633D ARG* 2.9 34.5 + - - +
634D ARG* 3.0 10.3 + - + -
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Residues in contact with GLU 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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630D VAL* 1.3 80.9 - - + +
632D PRO* 1.4 69.6 - - + +
634D ARG* 3.1 13.5 + - - +
635D GLU* 2.8 51.9 + - - +
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Residues in contact with PRO 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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624D MET* 4.2 28.5 - - + +
629D ARG* 3.7 33.9 - - + +
630D VAL 3.5 3.8 - - - -
631D GLU* 1.4 94.1 - - + +
633D ARG* 1.3 56.2 + - - +
635D GLU* 3.7 11.3 - - + +
636D PHE* 2.9 29.8 + - - +
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Residues in contact with ARG 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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19A PHE* 3.4 32.7 - - + -
174A VAL* 4.3 11.2 - - + -
175A GLY* 4.8 12.1 - - - +
624D MET* 3.7 12.0 + - - +
625D LEU* 2.4 31.3 + - + +
626D MET* 3.9 1.2 - - - +
627D GLY 2.4 37.8 + - - +
628D ASP 5.0 0.2 + - - -
629D ARG 3.0 23.8 + - - +
630D VAL* 2.9 39.6 + - - +
632D PRO* 1.3 76.8 - - - +
634D ARG* 1.3 58.9 + - - +
636D PHE* 3.4 6.6 + - + +
637D ILE* 2.9 29.7 + - + +
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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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175A GLY* 3.6 26.9 - - - +
176A MET* 5.5 3.4 - - + -
630D VAL* 3.0 10.1 + - + +
631D GLU* 3.5 21.5 - - - +
633D ARG* 1.3 74.5 - - - +
635D GLU* 1.3 60.3 + - + +
637D ILE* 3.4 7.8 + - - +
638D GLU* 2.9 28.6 + - - +
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Residues in contact with GLU 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 GLU* 2.8 39.4 + - - +
632D PRO* 3.7 10.7 - - + +
634D ARG* 1.3 74.3 - - - +
636D PHE* 1.3 59.2 + - - +
638D GLU* 3.1 8.2 + - - +
639D GLU* 2.9 31.5 + - - +
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Residues in contact with PHE 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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16A LYS* 4.1 31.9 - - + -
19A PHE* 4.4 14.6 - + - -
20A ILE* 4.9 8.5 - - + -
624D MET* 4.0 23.6 - - + -
625D LEU* 3.6 29.6 - - + -
632D PRO 2.9 18.9 + - - +
633D ARG* 3.6 8.1 - - - +
634D ARG 3.3 0.2 - - - -
635D GLU* 1.3 75.2 - - - +
637D ILE* 1.3 61.8 + - - +
639D GLU* 4.6 4.3 - - + -
640D ASN* 2.9 51.1 + - + +
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Residues in contact with ILE 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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19A PHE* 6.3 1.8 - - + -
23A ALA* 5.6 7.0 - - + -
27A ILE* 4.9 17.3 - - + -
174A VAL 5.2 5.8 - - - +
176A MET* 5.6 4.7 - - + -
633D ARG* 2.9 18.9 + - + +
634D ARG* 3.5 9.0 - - - +
636D PHE* 1.3 82.4 - - + +
638D GLU* 1.3 61.9 + - - +
639D GLU 3.4 0.3 + - - -
640D ASN 5.6 0.2 - - - -
641D ALA* 3.1 29.5 - - + +
643D TYR* 4.3 8.5 + - - +
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Residues in contact with GLU 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 GLU* 3.1 8.9 + - - +
637D ILE* 1.3 77.7 - - - +
639D GLU* 1.3 60.1 + - - +
641D ALA 4.6 6.3 - - - +
643D TYR* 5.7 5.2 - - - -
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Residues in contact with GLU 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 GLU 2.9 16.1 + - - +
636D PHE* 3.9 4.7 - - + +
638D GLU* 1.3 79.7 - - - +
640D ASN* 1.3 59.2 + - + +
641D ALA 3.3 8.0 + - - +
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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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20A ILE* 4.7 12.5 - - + +
636D PHE* 2.9 45.1 + - + +
637D ILE* 5.6 0.2 - - - -
639D GLU* 1.3 72.9 - - + +
641D ALA* 1.3 58.8 + - - +
642D VAL 4.4 0.2 + - - -
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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