Contacts of the helix formed by residues 709 - 722 (chain A) in PDB entry 4FUL
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 TYR 709 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499A ALA 2.6 31.2 + - - -
500A ASP* 3.8 13.9 - - - -
502A LEU 3.7 1.6 - - - -
503A THR* 3.3 29.4 + - - -
668A LYS* 3.1 58.2 + - + -
706A SER* 3.1 16.9 + - - +
708A HIS* 1.4 90.4 - - + +
710A GLN* 1.3 65.1 + - - +
711A GLN 3.1 3.6 + - - -
712A ARG* 3.4 29.5 + - + +
713A PHE* 3.0 43.7 + + + +
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Residues in contact with GLN 710 (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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160A TYR* 4.1 28.5 - - + -
508A PRO* 5.0 5.7 - - - +
703A ILE* 2.9 45.4 + - + +
704A ALA 4.8 4.6 + - - -
705A GLN 5.2 0.4 - - - -
706A SER* 2.8 26.8 + - - +
707A ARG* 3.2 33.1 + - - +
709A TYR* 1.3 71.8 - - - +
711A GLN* 1.3 59.7 + - + +
713A PHE* 4.6 0.2 - - - -
714A ALA* 2.7 38.4 + - - +
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Residues in contact with GLN 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A TYR* 3.2 34.5 + - + +
162A VAL* 4.8 0.3 - - - +
164A ASP 5.4 3.6 + - - -
167A ASN* 3.3 46.8 + - - +
168A VAL* 3.9 4.9 - - - +
173A LEU* 3.6 34.7 - - + +
505A ALA* 4.0 18.7 - - + +
673A HIS* 5.7 2.0 - - + -
707A ARG 4.9 4.5 + - - +
709A TYR 3.2 1.4 - - - -
710A GLN* 1.3 82.2 - - + +
712A ARG* 1.3 62.7 - - - +
714A ALA* 3.2 2.9 + - - +
715A VAL* 3.1 26.9 + - - +
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Residues in contact with ARG 712 (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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173A LEU* 3.8 11.7 - - - +
504A SER* 4.8 5.9 + - - +
667A VAL* 2.8 45.7 + - + -
668A LYS 4.3 5.3 + - - -
670A GLU* 2.7 33.5 + - - +
671A PRO 3.4 15.8 + - - -
672A TYR 3.4 16.7 - - - -
673A HIS* 3.0 42.7 + - + +
709A TYR* 3.4 29.7 + - + +
711A GLN* 1.3 75.4 - - - +
713A PHE* 1.4 65.8 + - + +
715A VAL* 3.2 13.4 + - - +
716A ILE* 3.2 27.6 + - + +
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Residues in contact with PHE 713 (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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664A VAL* 3.2 33.7 - - + -
665A GLN* 4.8 0.2 - - - -
667A VAL* 3.5 26.5 - - + -
668A LYS* 4.0 20.2 - - + -
699A LEU* 3.5 31.7 - - + +
702A GLU* 3.5 31.6 - - + -
703A ILE* 3.6 24.1 - - + +
709A TYR* 3.0 37.8 + + + +
712A ARG* 1.4 80.7 - - + +
714A ALA* 1.4 55.7 + - - +
716A ILE* 3.3 13.6 + - + +
717A LEU* 3.0 24.4 + - - +
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Residues in contact with ALA 714 (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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158A ILE* 3.7 16.5 - - + +
160A TYR* 3.6 21.1 - - + -
162A VAL* 3.4 23.7 - - + +
703A ILE* 3.5 12.3 - - + +
710A GLN 2.7 23.9 + - - +
711A GLN 3.2 4.5 + - - +
713A PHE* 1.4 73.0 - - - +
715A VAL* 1.3 60.0 + - - +
717A LEU* 3.5 2.1 + - - +
718A GLU* 3.1 18.9 + - - +
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Residues in contact with VAL 715 (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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162A VAL* 3.8 19.5 - - + +
173A LEU* 3.7 23.3 - - + -
176A THR* 3.8 31.0 - - + -
177A ARG* 3.8 35.8 - - + +
180A LEU* 4.2 3.8 - - + -
673A HIS* 5.8 0.4 - - + -
711A GLN 3.1 13.4 + - - +
712A ARG* 3.2 9.1 + - - +
714A ALA* 1.3 75.0 - - - +
716A ILE* 1.3 65.0 + - + +
718A GLU* 3.5 6.1 + - - +
719A ALA* 3.2 20.8 + - - +
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Residues in contact with ILE 716 (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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176A THR* 5.9 0.4 - - + -
180A LEU* 4.3 16.2 - - + -
667A VAL* 3.9 29.8 - - + -
673A HIS 4.8 4.9 - - - +
678A ALA* 4.0 36.6 - - + +
681A LEU* 5.5 4.9 - - + -
682A LEU* 4.4 13.4 - - + +
695A LEU* 5.4 4.0 - - + -
699A LEU* 4.0 18.6 - - + -
712A ARG* 3.2 21.2 + - + +
713A PHE* 3.3 16.8 + - + +
715A VAL* 1.3 77.3 - - + +
717A LEU* 1.4 57.0 + - - +
719A ALA* 3.2 5.7 + - - +
720A TYR* 3.0 24.7 + - + +
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Residues in contact with LEU 717 (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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158A ILE* 3.9 28.0 - - + -
696A PHE* 3.4 44.9 - - + +
699A LEU* 3.7 21.8 - - + +
700A ARG* 4.1 17.9 - - + +
703A ILE* 3.7 21.5 - - + -
713A PHE 3.0 15.8 + - - +
714A ALA 3.9 4.3 - - - +
716A ILE* 1.4 72.4 - - - +
718A GLU* 1.4 53.1 + - - +
720A TYR* 3.1 12.4 + - + +
721A LEU* 2.7 42.1 + - + +
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Residues in contact with GLU 718 (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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151A GLN* 3.5 4.7 - - - +
154A LEU* 4.5 7.2 - - + -
158A ILE* 3.7 23.8 - - + +
162A VAL* 3.7 13.6 - - + +
177A ARG* 2.7 56.6 + - - +
714A ALA 3.1 11.0 + - - +
715A VAL 3.7 8.7 - - - +
717A LEU* 1.4 72.8 - - - +
719A ALA* 1.4 53.9 + - - +
721A LEU* 3.0 6.8 + - - +
722A ARG* 2.8 66.4 + - + +
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Residues in contact with ALA 719 (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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177A ARG* 6.0 0.7 - - - +
180A LEU* 3.9 34.3 - - + +
184A ARG* 3.2 36.5 - - - +
682A LEU* 3.4 18.9 - - + +
686A LEU* 4.7 0.3 - - - +
715A VAL 3.2 10.1 + - - +
716A ILE* 3.2 10.4 + - - +
718A GLU* 1.4 79.1 + - - +
720A TYR* 1.4 60.7 + - - +
722A ARG* 3.5 1.5 + - - +
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Residues in contact with TYR 720 (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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196A TYR* 5.4 0.4 - - - -
682A LEU* 3.3 13.4 - - + +
685A GLY* 3.4 34.5 + - - -
686A LEU* 3.6 15.6 - - + +
692A GLY* 3.2 36.0 - - - -
695A LEU* 4.4 15.7 - - + -
696A PHE* 4.4 2.9 - - + -
699A LEU* 5.2 0.7 - - + -
716A ILE* 3.0 12.8 + - + +
717A LEU* 3.1 20.4 + - + +
719A ALA* 1.4 74.3 - - - +
721A LEU* 1.3 73.5 + - + +
723A GLY 3.3 2.6 + - - -
724A CYS* 3.1 41.8 + - + +
728A MET* 3.5 22.7 - - - +
732A PHE* 3.6 20.6 - + - -
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Residues in contact with LEU 721 (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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150A PHE* 4.9 0.3 - - - -
154A LEU* 3.6 22.7 - - + +
157A LEU* 3.6 31.9 - - + -
158A ILE* 3.8 24.0 - - + -
696A PHE* 3.7 31.2 - - + -
717A LEU* 2.7 23.1 + - + +
718A GLU 3.0 2.6 + - - +
720A TYR* 1.3 79.2 - - + +
722A ARG* 1.3 57.5 + - - +
723A GLY 3.3 3.7 + - - -
724A CYS* 3.6 6.9 + - - -
725A GLY 5.1 0.2 + - - -
729A LEU* 3.4 34.3 - - + +
732A PHE* 4.0 17.0 - - + -
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Residues in contact with ARG 722 (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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150A PHE* 3.6 31.8 - - + -
151A GLN* 2.7 31.1 + - - +
154A LEU* 3.5 15.1 - - + +
177A ARG* 3.9 5.8 - - - +
184A ARG* 3.5 47.4 + - - +
318A VAL* 3.4 19.2 - - - +
319A ARG* 4.6 8.6 - - - +
321A GLU* 4.7 14.3 - - - +
718A GLU* 2.8 46.9 + - + +
719A ALA* 5.5 0.2 - - - +
720A TYR 3.2 1.0 - - - -
721A LEU* 1.3 71.8 - - - +
723A GLY* 1.3 55.3 + - - +
725A GLY 5.6 0.4 - - - -
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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