Contacts of the helix formed by residues 699 - 708 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122D PHE* 3.5 14.7 - - - -
488D GLN* 3.5 24.9 - - - -
491D PHE* 4.7 1.7 - - - -
584D TYR* 5.4 1.1 - - - -
695D LEU 3.8 2.2 + - - -
696D ARG 3.9 5.9 + - - -
697D CYS 3.4 2.2 - - - -
698D ASN* 1.3 76.9 - - - +
700D VAL* 1.3 57.1 + - - +
701D LEU 3.2 2.7 - - - -
702D GLU* 2.9 9.1 + - - +
703D GLY* 2.8 26.9 + - - -
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Residues in contact with VAL 700 (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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91D MET* 5.8 0.7 - - + -
102D VAL* 4.6 8.1 - - + -
106D LEU* 6.2 1.1 - - + -
119D SER* 3.9 14.8 - - - +
122D PHE* 3.4 30.2 - - + -
124D VAL* 4.2 21.3 - - + -
673D ARG* 4.7 3.6 - - + -
695D LEU* 3.7 19.3 - - + +
698D ASN* 3.4 20.1 - - + +
699D GLY* 1.3 78.1 - - - +
701D LEU* 1.3 78.2 + - + +
703D GLY* 3.2 1.4 + - - -
704D ILE* 3.2 26.4 + - + +
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Residues in contact with LEU 701 (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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98D HIS 5.2 2.7 - - - +
99D GLU* 3.6 37.2 - - + +
102D VAL* 4.4 17.3 - - + -
692D LEU* 4.6 2.0 - - + +
695D LEU* 3.0 44.7 + - + +
696D ARG* 4.0 20.9 - - + +
700D VAL* 1.3 93.9 - - + +
702D GLU* 1.3 59.4 + - - +
704D ILE* 3.9 11.3 - - + +
705D ARG* 3.2 42.7 + - - +
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Residues in contact with GLU 702 (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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488D GLN* 4.9 11.0 - - - +
491D PHE* 5.4 0.4 - - - -
492D ASN* 3.7 21.3 + - - +
518D ASP* 5.9 1.6 - - - +
519D LEU* 4.8 3.8 - - - +
584D TYR* 4.4 27.2 - - + +
696D ARG 5.4 5.0 + - - +
699D GLY* 2.9 16.2 + - - +
701D LEU* 1.3 78.6 - - - +
703D GLY* 1.3 62.7 + - - +
704D ILE 3.2 0.7 - - - -
705D ARG* 3.4 18.0 - - - +
706D ILE* 3.1 46.5 + - + +
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Residues in contact with GLY 703 (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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119D SER 5.7 1.1 - - - -
122D PHE* 4.8 3.8 - - - -
491D PHE* 4.3 20.2 - - - -
495D MET* 4.3 7.1 - - - +
699D GLY 2.8 15.3 + - - -
700D VAL 3.2 2.8 + - - -
702D GLU* 1.3 77.5 - - - +
704D ILE* 1.3 68.4 + - - +
706D ILE* 3.8 6.5 + - - +
707D CYS* 3.1 29.4 + - - +
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Residues in contact with ILE 704 (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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91D MET* 5.8 1.3 - - + +
92D ALA* 4.8 14.1 - - + +
97D LEU* 4.2 37.7 - - + +
98D HIS 4.8 6.5 - - - +
102D VAL* 4.3 19.5 - - + -
119D SER* 3.1 36.8 - - - +
120D GLY* 5.7 0.2 - - - -
700D VAL* 3.2 16.1 + - + +
701D LEU* 3.9 15.0 - - + +
702D GLU 3.2 0.2 - - - -
703D GLY* 1.3 80.4 - - - +
705D ARG* 1.3 63.0 + - - +
707D CYS* 3.0 8.4 + - + +
708D ARG* 2.9 35.5 + - - +
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Residues in contact with ARG 705 (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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99D GLU* 4.2 18.3 + - - -
696D ARG* 6.0 2.6 - - - +
701D LEU* 3.2 36.1 + - - +
702D GLU* 3.4 26.2 - - - +
704D ILE* 1.3 83.3 - - - +
706D ILE* 1.3 64.5 + - + +
708D ARG* 3.0 52.0 + - - +
709D LYS* 3.3 19.9 + - + +
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Residues in contact with ILE 706 (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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491D PHE* 5.0 2.0 - - + -
492D ASN* 4.1 25.1 - - + +
495D MET* 3.7 23.8 - - - -
499D GLU* 4.9 9.0 - - + +
515D PHE* 3.7 60.3 - - + -
702D GLU* 3.1 31.2 + - - +
703D GLY* 3.9 7.2 - - - +
705D ARG* 1.3 80.7 - - + +
707D CYS* 1.3 63.4 + - - +
709D LYS* 3.6 21.2 + - + +
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Residues in contact with CYS 707 (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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92D ALA* 4.7 20.0 - - + -
97D LEU* 4.9 10.8 - - + -
120D GLY* 5.8 1.3 - - - -
495D MET* 4.0 22.0 - - - -
499D GLU* 5.2 10.7 - - - +
503D TYR* 5.5 1.6 + - - -
703D GLY 3.1 19.1 + - - +
704D ILE* 3.0 14.8 + - + +
706D ILE* 1.3 77.1 - - - +
708D ARG* 1.3 57.9 + - - +
709D LYS 2.9 11.9 + - - -
710D GLY* 3.1 12.8 + - - -
714D ARG* 5.6 2.9 + - - -
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Residues in contact with ARG 708 (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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97D LEU* 2.8 58.5 + - + -
98D HIS* 4.3 8.3 - - - +
99D GLU 5.2 0.2 - - - +
704D ILE* 2.9 18.8 + - - +
705D ARG* 3.0 46.4 + - - +
707D CYS* 1.3 72.8 - - - +
709D LYS* 1.3 56.5 + - + +
710D GLY 2.2 24.2 + - - +
768D MLY 5.0 6.4 + - - -
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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