Contacts of the helix formed by residues 98 - 109 (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 HIS 98 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D PHE* 4.4 2.0 - + - -
78D PHE* 3.1 42.2 - + + +
79D SER* 2.8 35.5 + - - -
80D MET* 4.8 0.9 - - - -
96D HIS* 3.3 29.1 + + + -
97D LEU* 1.3 76.9 - - - +
99D GLU* 1.3 66.7 + - - +
100D PRO* 3.2 13.0 - - + -
101D ALA* 3.2 25.9 + - + +
102D VAL* 3.5 20.1 + - - +
701D LEU* 5.2 1.3 - - - +
704D ILE* 4.8 5.6 - - - +
708D ARG* 4.3 8.1 - - - +
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Residues in contact with GLU 99 (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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47D PHE* 3.9 21.3 - - + -
78D PHE* 5.6 3.5 - - + -
98D HIS* 1.3 76.2 - - - +
100D PRO* 1.3 72.0 - - + +
102D VAL* 3.2 13.1 + - - +
103D LEU* 3.3 12.2 + - - +
692D LEU* 4.2 10.6 - - + +
695D LEU* 5.4 0.3 - - - +
696D ARG* 2.3 43.9 + - - -
701D LEU* 3.6 28.6 - - + +
705D ARG* 4.2 19.8 + - - -
708D ARG* 5.2 0.8 - - - +
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Residues in contact with PRO 100 (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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39D PHE* 3.7 26.9 - - + -
47D PHE* 3.6 46.0 - - + -
78D PHE* 3.8 20.4 - - + -
98D HIS* 3.2 12.3 - - + -
99D GLU* 1.3 93.6 - - + +
101D ALA* 1.3 65.4 + - - +
102D VAL 2.9 0.7 + - - -
103D LEU* 3.0 6.2 + - + +
104D TYR* 2.8 29.0 + - + +
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Residues in contact with ALA 101 (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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39D PHE* 3.9 16.3 - - + -
81D ASN* 3.5 9.6 - - - +
94D MET* 3.0 36.0 - - + +
96D HIS 3.6 4.0 - - - +
98D HIS* 3.2 29.0 + - + +
99D GLU 3.4 0.8 - - - -
100D PRO* 1.3 79.4 - - - +
102D VAL* 1.3 57.9 + - + +
104D TYR* 4.0 0.6 - - - +
105D ASN* 3.1 22.7 + - - +
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Residues in contact with VAL 102 (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* 3.9 31.9 - - + +
94D MET* 4.9 5.6 - - + -
96D HIS 5.7 0.4 - - - +
97D LEU* 5.7 2.2 - - + -
98D HIS 3.5 17.7 - - - +
99D GLU 3.2 8.9 + - - +
100D PRO 2.9 1.2 - - - -
101D ALA* 1.3 78.2 - - - +
103D LEU* 1.3 70.5 + - - +
106D LEU* 3.3 23.3 + - + +
119D SER* 5.4 0.4 - - - +
695D LEU* 3.8 22.4 - - + -
700D VAL* 4.6 9.2 - - + -
701D LEU* 4.4 10.8 - - + -
704D ILE* 4.3 22.4 - - + -
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Residues in contact with LEU 103 (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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46D SER* 5.0 0.4 - - - -
47D PHE* 4.8 8.3 - - + -
99D GLU 3.3 8.7 + - - +
100D PRO* 3.0 7.8 + - + +
102D VAL* 1.3 85.2 - - - +
104D TYR* 1.3 76.8 + - + +
106D LEU* 3.1 2.9 + - - +
107D MLY 3.0 20.3 + - + +
686D MET* 3.5 23.6 - - + -
688D HIS* 4.0 32.5 - - + +
691D VAL* 4.5 16.4 - - + -
692D LEU* 3.6 39.0 - - + +
695D LEU* 4.7 5.6 - - + +
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Residues in contact with TYR 104 (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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39D PHE* 3.5 37.5 - + + -
47D PHE* 2.5 39.2 + - + -
48D VAL* 3.1 20.5 - - - +
49D MLY 4.3 23.8 - - + -
100D PRO* 2.8 22.9 + - + +
101D ALA 4.3 1.6 - - - +
103D LEU* 1.3 88.3 - - + +
105D ASN* 1.3 55.6 + - - +
107D MLY 3.7 33.1 - - + +
108D GLU* 3.0 43.0 + - + +
688D HIS* 3.6 18.9 - + - -
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Residues in contact with ASN 105 (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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85D TYR 4.5 2.4 - - - +
86D ASP 2.9 28.6 - - - +
87D MLY 3.5 0.6 - - - -
88D ILE* 3.1 40.1 + - - +
91D MET* 3.4 28.7 - - + +
94D MET* 4.8 8.1 - - + +
101D ALA 3.1 18.9 + - - +
103D LEU 3.2 0.6 + - - -
104D TYR* 1.3 73.0 - - - +
106D LEU* 1.3 66.9 + - - +
108D GLU* 3.5 2.6 + - - +
109D ARG* 2.9 37.8 + - - +
117D THR* 4.0 1.0 + - - -
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Residues in contact with LEU 106 (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* 3.1 32.3 - - + -
102D VAL* 3.3 23.1 + - + +
103D LEU* 3.1 8.5 + - - +
105D ASN* 1.3 83.2 - - - +
107D MLY 1.3 64.3 + - - +
109D ARG* 3.0 13.8 + - - +
110D TYR* 3.2 14.8 + - - +
114D MET 5.0 0.7 - - - +
117D THR* 3.4 26.8 - - + +
124D VAL* 4.4 17.7 - - + -
126D VAL* 5.1 8.2 - - + +
675D ILE* 5.4 1.8 - - + -
686D MET* 4.1 9.4 - - + -
691D VAL* 4.6 9.0 - - + -
695D LEU* 4.4 22.9 - - + -
700D VAL* 6.2 0.9 - - + -
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Residues in contact with MLY 107 (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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45D GLN* 4.9 9.6 - - - -
103D LEU* 3.0 8.9 + - + +
104D TYR* 3.7 32.5 - - + +
106D LEU* 1.3 80.0 + - - +
108D GLU* 1.3 67.1 + - + +
110D TYR* 3.2 5.8 + - + +
111D ALA* 3.1 23.8 + - + +
686D MET* 3.0 48.6 - - + +
688D HIS* 2.9 41.3 + - + +
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Residues in contact with GLU 108 (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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49D MLY 2.8 47.4 - - - -
86D ASP* 3.7 29.7 - - - +
87D MLY 4.2 20.7 - - + -
104D TYR* 3.0 31.3 + - + +
105D ASN* 3.5 3.1 + - - +
106D LEU 3.2 0.4 + - - -
107D MLY 1.3 81.4 + - + +
109D ARG* 1.3 58.1 + - - +
110D TYR 3.1 4.2 + - - -
111D ALA* 3.4 14.7 + - + +
112D ALA* 3.5 11.6 + - - +
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Residues in contact with ARG 109 (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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17D LEU 4.2 8.5 + - - -
18D ARG* 5.8 0.4 - - - +
87D MLY 2.9 46.3 + - + +
88D ILE 3.9 3.6 + - - -
89D GLU* 3.7 19.5 + - - +
105D ASN* 2.9 32.5 + - - +
106D LEU* 3.0 4.7 + - - +
108D GLU* 1.3 74.9 - - - +
110D TYR* 1.3 51.3 + - - +
112D ALA* 3.9 4.5 - - - -
113D TRP 3.7 0.2 + - - -
114D MET* 2.4 83.0 + - - +
116D TYR 2.8 29.7 + - - -
117D THR* 3.4 32.4 - - + +
153D PRO* 4.2 3.2 - - - +
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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