Contacts of the helix formed by residues 699 - 708 (chain J) in PDB entry 1MVW
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 699 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122J PHE* 3.5 15.0 - - - -
488J GLN* 3.5 24.2 - - - -
491J PHE* 4.7 1.7 - - - -
584J TYR* 5.4 1.1 - - - -
695J LEU 3.8 2.4 + - - -
696J ARG 3.8 5.7 + - - -
697J CYS 3.4 1.8 - - - -
698J ASN* 1.3 76.7 - - - +
700J VAL* 1.3 58.3 + - - +
701J LEU 3.2 2.7 - - - -
702J GLU* 2.9 9.4 + - - +
703J GLY* 2.8 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 700 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91J MET* 5.8 0.4 - - + -
102J VAL* 4.6 8.5 - - + -
119J SER* 3.9 14.6 - - - +
122J PHE* 3.4 31.1 - - + -
124J VAL* 4.2 20.9 - - + -
673J ARG* 4.7 4.3 - - + -
695J LEU* 3.7 18.6 - - + +
698J ASN* 3.4 20.3 - - + +
699J GLY* 1.3 78.6 - - - +
701J LEU* 1.3 79.1 + - + +
703J GLY* 3.2 1.4 + - - -
704J ILE* 3.2 26.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 701 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98J HIS 5.2 2.5 - - - +
99J GLU* 3.6 38.1 - - + +
102J VAL* 4.4 18.2 - - + -
692J LEU* 4.6 2.2 - - + +
695J LEU* 3.0 44.0 + - + +
696J ARG* 4.0 20.9 - - + +
700J VAL* 1.3 93.7 - - + +
702J GLU* 1.3 60.9 + - - +
704J ILE* 3.9 11.1 - - + +
705J ARG* 3.2 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 702 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488J GLN* 4.9 10.9 - - - +
491J PHE* 5.4 0.4 - - - -
492J ASN* 3.7 19.9 + - - +
518J ASP* 5.9 1.2 - - - +
519J LEU* 4.8 4.5 - - - +
584J TYR* 4.4 27.5 - - + +
696J ARG 5.4 5.3 + - - +
699J GLY* 2.9 14.5 + - - +
701J LEU* 1.3 79.3 - - - +
703J GLY* 1.3 64.2 + - - +
704J ILE 3.2 0.7 - - - -
705J ARG* 3.5 17.9 - - - +
706J ILE* 3.1 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 703 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J SER 5.7 0.9 - - - -
122J PHE* 4.8 3.4 - - - -
491J PHE* 4.3 20.2 - - - -
495J MET* 4.3 6.5 - - - +
699J GLY 2.8 13.6 + - - -
700J VAL 3.2 2.9 + - - -
702J GLU* 1.3 78.9 - - - +
704J ILE* 1.3 66.9 + - - +
706J ILE* 3.9 6.1 - - - +
707J CYS* 3.1 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 704 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91J MET* 5.8 1.3 - - + +
92J ALA* 4.8 14.4 - - + +
97J LEU* 4.2 37.7 - - + +
98J HIS 4.8 7.4 - - - +
102J VAL* 4.3 18.8 - - + -
119J SER* 3.1 35.9 - - - +
700J VAL* 3.2 14.7 + - + +
701J LEU* 3.9 14.6 - - + +
702J GLU 3.2 0.2 - - - -
703J GLY* 1.3 80.0 - - - +
705J ARG* 1.3 61.6 + - - +
707J CYS* 3.0 8.8 + - + +
708J ARG* 2.9 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 705 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99J GLU* 4.2 18.5 + - - -
696J ARG* 6.0 2.8 - - - +
701J LEU* 3.2 37.6 + - - +
702J GLU* 3.5 25.5 - - - +
704J ILE* 1.3 82.8 - - - +
706J ILE* 1.3 64.1 + - + +
708J ARG* 3.0 52.5 + - - +
709J LYS* 3.3 19.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 706 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491J PHE* 5.0 2.5 - - + -
492J ASN* 4.1 24.9 - - + +
495J MET* 3.7 24.0 - - - -
499J GLU* 4.9 8.7 - - + +
515J PHE* 3.7 60.6 - - + -
702J GLU* 3.1 30.5 - - - +
703J GLY* 3.9 7.2 - - - +
705J ARG* 1.3 81.2 - - + +
707J CYS* 1.3 62.7 + - - +
709J LYS* 3.6 19.9 + - + +
714J ARG* 4.8 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 707 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92J ALA* 4.7 17.3 - - + -
97J LEU* 4.9 4.3 - - + -
120J GLY* 5.8 1.6 - - - -
495J MET* 4.0 17.7 - - - -
499J GLU* 5.2 1.0 - - - +
703J GLY 3.1 18.9 + - - +
704J ILE* 3.0 14.6 + - + +
705J ARG 2.9 0.2 - - - -
706J ILE* 1.3 77.4 - - - +
708J ARG* 1.3 59.2 + - - +
709J LYS 2.9 11.2 + - - -
710J GLY* 4.3 0.2 - - - -
711J PHE 3.7 5.2 + - - -
712J PRO* 3.6 11.9 - - + +
714J ARG* 2.7 53.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 708 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J LEU* 2.8 44.3 + - + -
98J HIS* 4.3 9.1 - - - +
99J GLU 5.2 0.2 - - - +
704J ILE* 2.9 19.3 + - - +
705J ARG* 3.0 46.4 + - - +
707J CYS* 1.3 74.6 - - - +
709J LYS* 1.3 60.6 + - + +
710J GLY 3.5 4.5 + - - -
712J PRO* 3.7 32.5 - - + +
770J GLY 4.7 12.0 + - - +
771J LEU* 5.5 3.8 + - - +
772J LEU 6.0 0.2 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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