Contacts of the helix formed by residues 98 - 109 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39G PHE* 4.4 0.9 - + - -
78G PHE* 3.1 41.9 - + + +
79G SER* 2.8 36.6 + - - -
80G MET* 4.8 1.1 - - - -
96G HIS* 3.3 27.9 + + + -
97G LEU* 1.3 77.5 - - - +
99G GLU* 1.3 67.2 + - - +
100G PRO* 3.2 13.0 - - + -
101G ALA* 3.2 25.1 + - + +
102G VAL* 3.5 19.9 + - - +
701G LEU* 5.2 1.3 - - - +
704G ILE* 4.8 5.9 - - - +
708G ARG* 4.3 7.6 - - - +
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Residues in contact with GLU 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G PHE* 3.9 21.4 - - + -
78G PHE* 5.6 3.7 - - + -
98G HIS* 1.3 76.2 - - - +
100G PRO* 1.3 72.9 - - + +
102G VAL* 3.2 14.0 + - - +
103G LEU* 3.3 12.0 + - - +
692G LEU* 4.2 10.0 - - + +
695G LEU* 5.4 0.2 - - - +
696G ARG* 2.3 43.2 + - - -
701G LEU* 3.6 28.9 - - + +
705G ARG* 4.2 20.1 + - - -
708G ARG* 5.2 1.0 - - - +
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Residues in contact with PRO 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G PHE* 3.7 26.7 - - + -
47G PHE* 3.6 46.0 - - + -
78G PHE* 3.8 21.1 - - + -
98G HIS* 3.2 12.3 - - + -
99G GLU* 1.3 95.2 - - + +
101G ALA* 1.3 65.0 + - - +
102G VAL 2.9 0.5 + - - -
103G LEU* 3.0 5.7 + - + +
104G TYR* 2.8 30.3 + - + +
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Residues in contact with ALA 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G PHE* 3.9 15.6 - - + -
81G ASN* 3.5 9.9 - - - +
94G MET* 3.0 36.2 - - + +
96G HIS 3.6 3.8 - - - +
98G HIS* 3.2 29.4 + - + +
99G GLU 3.4 0.6 - - - -
100G PRO* 1.3 78.9 - - - +
102G VAL* 1.3 57.9 + - - +
104G TYR* 4.0 0.7 - - - +
105G ASN* 3.1 22.2 + - - +
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Residues in contact with VAL 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G MET* 3.9 31.0 - - + +
94G MET* 4.8 5.6 - - + -
96G HIS 5.7 0.4 - - - +
97G LEU* 5.7 2.2 - - + -
98G HIS 3.5 17.9 + - - +
99G GLU 3.2 8.2 + - - +
100G PRO 2.9 1.0 - - - -
101G ALA* 1.3 77.6 - - - +
103G LEU* 1.3 72.9 + - - +
105G ASN 3.4 0.3 + - - -
106G LEU* 3.3 23.7 + - + +
119G SER* 5.4 0.2 - - - +
695G LEU* 3.8 21.5 - - + -
700G VAL* 4.6 8.7 - - + -
701G LEU* 4.4 11.7 - - + -
704G ILE* 4.3 22.7 - - + -
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Residues in contact with LEU 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G SER* 5.0 0.7 - - - -
47G PHE* 4.8 7.9 - - + -
99G GLU 3.3 8.5 + - - +
100G PRO* 3.0 7.6 + - + +
102G VAL* 1.3 86.4 - - - +
104G TYR* 1.3 76.4 + - + +
106G LEU* 3.1 3.5 + - - +
107G MLY 3.0 21.0 + - + +
686G MET* 3.5 22.4 - - + -
688G HIS* 4.0 33.2 - - + +
691G VAL* 4.5 16.4 - - + -
692G LEU* 3.7 38.8 - - + -
695G LEU* 4.7 5.8 - - + -
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Residues in contact with TYR 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G PHE* 3.5 36.3 - + + -
47G PHE* 2.5 38.6 + - + -
48G VAL* 3.1 21.0 - - - +
49G MLY 4.3 23.1 - - + -
100G PRO* 2.8 23.4 + - + +
101G ALA* 4.3 2.0 - - - +
103G LEU* 1.3 87.4 - - + +
105G ASN* 1.3 55.6 + - - +
107G MLY 3.6 33.0 + - + +
108G GLU* 3.1 42.6 + - + +
688G HIS* 3.6 18.9 - + - -
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Residues in contact with ASN 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85G TYR 4.5 2.8 - - - +
86G ASP 2.9 28.1 - - - +
87G MLY 4.3 0.9 - - - -
88G ILE* 3.1 40.8 + - - +
91G MET* 3.4 27.8 - - + +
94G MET* 4.8 7.9 - - + +
101G ALA 3.1 19.6 + - - +
103G LEU 3.2 0.4 + - - -
104G TYR* 1.3 74.3 - - - +
106G LEU* 1.3 67.3 + - - +
108G GLU* 3.5 2.7 + - - +
109G ARG* 2.9 37.5 + - - +
117G THR* 4.0 1.0 + - - -
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Residues in contact with LEU 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G MET* 3.1 33.2 - - + -
102G VAL* 3.3 23.5 + - + +
103G LEU* 3.1 8.5 + - - +
105G ASN* 1.3 81.7 - - - +
107G MLY 1.3 67.4 + - - +
109G ARG* 3.0 14.4 + - - +
110G TYR* 3.2 14.6 + - - +
114G MET 5.0 0.7 - - - +
117G THR* 3.4 26.8 - - + +
124G VAL* 4.4 17.0 - - + -
126G VAL* 5.1 9.1 - - + +
675G ILE* 5.4 1.8 - - + -
686G MET* 4.1 9.4 - - + -
691G VAL* 4.6 9.4 - - + -
695G LEU* 4.4 22.4 - - + -
700G VAL* 6.2 0.9 - - + -
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Residues in contact with MLY 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G GLN* 4.9 9.4 - - - -
48G VAL* 6.5 0.2 - - - -
103G LEU* 3.0 9.5 + - + +
104G TYR* 3.7 34.5 - - + +
106G LEU* 1.3 80.7 + - - +
108G GLU* 1.3 65.7 + - + +
110G TYR* 3.2 5.6 + - + +
111G ALA* 3.1 23.8 + - + +
686G MET* 3.0 48.2 - - + +
688G HIS* 2.9 41.3 + - + +
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Residues in contact with GLU 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G MLY 2.8 48.9 - - - -
86G ASP* 3.7 29.4 - - - +
87G MLY 4.2 20.7 - - + -
104G TYR* 3.1 30.9 + - + +
105G ASN* 4.3 3.1 - - - +
106G LEU 3.2 0.4 + - - -
107G MLY 1.3 82.2 + - + +
109G ARG* 1.3 57.5 + - - +
110G TYR 3.1 4.2 + - - -
111G ALA* 3.4 14.6 + - - +
112G ALA* 3.5 11.8 + - - +
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Residues in contact with ARG 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G LEU 4.2 8.5 + - - -
18G ARG* 6.0 0.4 - - - +
87G MLY 2.9 46.0 + - + -
88G ILE 4.1 3.8 - - - -
89G GLU* 3.7 19.4 + - - +
105G ASN* 2.9 33.8 + - - +
106G LEU 3.0 4.9 + - - +
108G GLU* 1.3 74.9 - - - +
110G TYR* 1.3 51.0 + - - +
112G ALA* 3.9 4.9 - - - -
113G TRP 3.7 0.2 + - - -
114G MET* 2.4 82.6 + - + +
116G TYR 2.8 30.5 + - - -
117G THR* 3.4 32.0 - - + +
153G PRO* 4.2 2.8 - - - +
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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