Contacts of the helix formed by residues 308 - 319 (chain 5) 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 308 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2195 VAL* 3.0 19.8 - - - +
2215 LEU* 4.7 5.6 - - - +
3075 PRO* 1.3 72.0 - - - +
3095 ILE* 1.3 63.4 + - - +
3105 ALA* 3.3 2.9 - - - +
3115 ASP* 4.0 22.2 - - - +
3125 ARG* 3.3 21.5 + - - +
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Residues in contact with ILE 309 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1535 LEU* 5.7 4.3 - - + -
2195 VAL* 3.9 15.3 - - + -
2615 LEU* 4.3 13.2 - - + -
2625 PHE* 4.6 8.8 - - + -
2745 ILE* 6.2 2.7 - - + -
2995 MET* 4.3 13.9 - - + -
3035 THR 3.9 7.6 - - - +
3045 THR* 3.2 50.7 - - + +
3065 TYR* 3.2 26.0 - - + +
3075 PRO 3.2 1.4 - - - -
3085 GLY* 1.3 78.0 - - - +
3105 ALA* 1.3 73.7 + - + +
3125 ARG* 3.8 2.4 + - - +
3135 MET* 3.0 32.8 + - + +
3355 ARG* 3.5 13.9 - - - +
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Residues in contact with ALA 310 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2995 MET* 4.0 22.4 - - + -
3085 GLY* 5.2 0.9 - - - +
3095 ILE* 1.3 83.3 - - + +
3115 ASP* 1.4 53.2 + - - +
3135 MET* 3.1 3.6 + - - +
3145 GLN* 2.8 39.5 + - + +
3295 ILE* 4.1 14.8 - - + +
3315 ALA* 4.1 13.7 - - + -
3355 ARG* 5.5 0.4 - - - +
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Residues in contact with ASP 311 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2215 LEU* 3.8 31.6 - - + +
3085 GLY* 3.8 16.7 + - - +
3095 ILE 3.5 0.2 - - - -
3105 ALA* 1.4 72.7 - - - +
3125 ARG* 1.3 66.3 + - - +
3145 GLN* 3.1 11.1 - - - +
3155 LYS* 3.0 26.5 + - - +
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Residues in contact with ARG 312 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2195 VAL* 3.6 12.3 - - + -
2205 ALA 3.0 21.4 + - - +
2215 LEU* 3.8 16.1 - - - +
2225 ASP 4.9 3.1 - - - +
2235 PHE* 2.9 42.5 - - - +
2625 PHE* 3.3 25.4 - - + +
2635 GLN* 3.4 26.7 + - - +
3085 GLY 3.3 15.2 + - - +
3095 ILE 3.8 2.9 - - - +
3115 ASP* 1.3 77.8 - - - +
3135 MET* 1.3 51.2 + - - +
3155 LYS* 3.3 3.9 + - - +
3165 GLU* 2.7 75.8 + - - +
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Residues in contact with MET 313 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1535 LEU* 4.5 9.2 - - + -
2625 PHE* 4.2 11.7 - - + -
2745 ILE* 3.8 17.3 - - + -
2755 HIS* 3.4 34.3 - - - -
2785 THR* 3.0 36.8 - - + +
2975 ASN* 4.4 11.0 - - - +
2995 MET* 4.8 8.1 - - - -
3095 ILE* 3.0 23.8 + - + +
3105 ALA* 3.1 4.5 + - - +
3125 ARG* 1.3 72.5 - - - +
3145 GLN* 1.3 59.8 + - - +
3165 GLU* 3.6 1.9 - - - +
3175 ILE* 2.9 39.1 + - + +
3295 ILE* 4.1 17.7 - - + -
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Residues in contact with GLN 314 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3105 ALA* 2.8 12.4 + - + +
3115 ASP* 3.1 17.3 - - - +
3135 MET* 1.3 75.1 - - - +
3155 LYS* 1.3 62.2 + - + +
3185 THR* 2.8 34.5 + - - +
3275 ILE* 3.5 31.4 + - - +
3285 LYS* 4.3 2.0 - - - +
3295 ILE* 3.5 30.5 + - + +
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Residues in contact with LYS 315 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2215 LEU* 6.3 3.8 - - + -
3115 ASP 3.0 13.2 + - - +
3125 ARG* 4.0 3.8 - - - +
3145 GLN* 1.3 82.6 - - + +
3165 GLU* 1.3 66.7 + - + +
3185 THR* 3.1 33.7 + - + +
3195 ALA* 3.5 30.1 - - - +
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Residues in contact with GLU 316 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2625 PHE* 4.6 2.5 - - + -
2755 HIS* 3.2 58.1 + - + -
3125 ARG* 2.7 60.1 + - - +
3135 MET* 3.2 7.8 + - - +
3155 LYS* 1.3 81.7 - - - +
3175 ILE* 1.3 62.3 + - - +
3195 ALA* 3.9 3.6 + - - +
3205 LEU* 3.8 17.0 + - - +
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Residues in contact with ILE 317 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2755 HIS* 3.8 22.2 - - + +
2785 THR* 4.1 17.3 - - + -
2795 TYR* 5.1 5.6 - - + +
2945 TYR* 4.0 25.1 - - + +
2975 ASN* 3.9 13.2 - - - +
3135 MET* 2.9 27.7 + - + +
3165 GLU* 1.3 76.8 - - - +
3185 THR* 1.3 66.4 + - - +
3195 ALA 3.2 2.0 - - - -
3205 LEU* 3.0 6.3 + - + +
3215 ALA* 2.9 25.8 + - - +
3275 ILE* 3.7 26.5 - - + -
3295 ILE* 3.6 21.8 - - + -
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Residues in contact with THR 318 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3145 GLN* 2.8 30.6 + - - +
3155 LYS* 3.1 30.1 + - + +
3175 ILE* 1.3 74.1 - - - +
3195 ALA* 1.3 60.9 + - - +
3205 LEU 3.1 5.5 + - - -
3215 ALA* 3.1 20.4 - - - +
3235 SER* 5.8 0.7 - - - -
3255 MET 6.1 0.4 - - - +
3275 ILE* 3.7 30.5 - - + -
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Residues in contact with ALA 319 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3155 LYS* 3.5 29.4 + - - +
3165 GLU 4.0 4.5 - - - +
3175 ILE 3.2 1.0 - - - -
3185 THR* 1.3 80.2 + - - +
3205 LEU* 1.3 59.0 + - - +
3215 ALA 4.8 0.7 - - - -
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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