Contacts of the helix formed by residues 308 - 319 (chain 7) 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 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2197 VAL* 3.0 17.7 - - - +
2217 LEU* 4.7 5.6 - - - +
3077 PRO* 1.3 72.9 - - - +
3097 ILE* 1.3 63.1 + - - +
3107 ALA* 3.3 4.0 - - - +
3117 ASP* 4.0 22.2 - - - +
3127 ARG* 3.3 21.8 + - - +
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Residues in contact with ILE 309 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1537 LEU* 5.7 4.5 - - + -
2197 VAL* 3.9 14.8 - - + -
2617 LEU* 4.3 13.7 - - + -
2627 PHE* 4.6 8.6 - - + -
2747 ILE* 6.2 3.4 - - + -
2997 MET* 4.3 13.5 - - + -
3037 THR 3.9 7.0 - - - +
3047 THR* 3.2 51.4 - - + +
3067 TYR* 3.2 27.1 - - + +
3077 PRO 3.2 1.2 + - - -
3087 GLY* 1.3 77.8 - - - +
3107 ALA* 1.3 74.2 + - + +
3127 ARG* 3.8 2.6 + - - +
3137 MET* 3.0 32.6 + - + +
3357 ARG* 3.5 14.1 - - - +
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Residues in contact with ALA 310 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2997 MET* 4.0 22.7 - - + -
3087 GLY* 5.7 1.1 - - - +
3097 ILE* 1.3 82.4 - - + +
3117 ASP* 1.4 53.7 + - - +
3137 MET* 3.1 3.8 + - - +
3147 GLN* 2.8 38.5 + - + +
3297 ILE* 4.1 15.2 - - + +
3317 ALA* 4.1 14.4 - - + -
3357 ARG* 5.5 0.4 - - - +
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Residues in contact with ASP 311 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2217 LEU* 3.8 32.7 - - + +
3087 GLY* 3.8 16.0 + - - +
3097 ILE 3.5 0.2 - - - -
3107 ALA* 1.4 74.1 - - - +
3127 ARG* 1.3 65.9 + - - +
3147 GLN* 3.1 10.6 - - - +
3157 LYS* 3.0 26.5 + - - +
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Residues in contact with ARG 312 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2197 VAL* 3.6 13.0 - - + -
2207 ALA 3.0 20.7 + - - +
2217 LEU* 3.8 14.8 - - - +
2227 ASP 4.9 3.7 - - - +
2237 PHE* 2.9 41.1 - - - +
2627 PHE* 3.3 26.0 - - + +
2637 GLN* 3.4 27.7 + - - +
3087 GLY 3.3 14.4 + - - +
3097 ILE 3.9 3.4 - - - +
3117 ASP* 1.3 77.7 - - - +
3137 MET* 1.3 53.0 + - - +
3157 LYS* 3.3 4.1 + - - +
3167 GLU* 2.7 77.3 + - - +
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Residues in contact with MET 313 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1537 LEU* 4.5 9.4 - - + -
2627 PHE* 4.2 11.4 - - + -
2747 ILE* 3.9 17.9 - - + -
2757 HIS* 3.4 33.9 - - - -
2787 THR* 3.0 37.0 - - + +
2977 ASN* 4.4 11.4 - - - +
2997 MET* 4.8 8.7 - - - -
3097 ILE* 3.0 22.5 + - + +
3107 ALA* 3.1 4.9 + - - +
3127 ARG* 1.3 71.7 - - - +
3147 GLN* 1.3 58.3 + - - +
3167 GLU* 3.6 1.6 - - - +
3177 ILE* 2.9 39.4 + - + +
3297 ILE* 4.1 17.5 - - + -
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Residues in contact with GLN 314 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3107 ALA* 2.8 13.1 + - + +
3117 ASP* 3.1 15.9 - - - +
3137 MET* 1.3 76.3 - - - +
3157 LYS* 1.3 62.0 + - + +
3187 THR* 2.8 35.3 + - - +
3277 ILE* 3.5 32.4 + - - +
3287 LYS* 4.3 2.2 - - - +
3297 ILE* 3.5 30.2 - - + +
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Residues in contact with LYS 315 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2217 LEU* 6.3 4.5 - - + -
3117 ASP 3.0 12.3 + - - +
3127 ARG* 4.0 3.6 - - - +
3147 GLN* 1.3 82.5 - - + +
3167 GLU* 1.3 67.5 + - + +
3187 THR* 3.1 34.4 + - + +
3197 ALA* 3.5 29.9 - - - +
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Residues in contact with GLU 316 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2627 PHE* 4.6 2.0 - - + -
2757 HIS* 3.2 57.0 + - + +
3127 ARG* 2.7 59.1 + - - +
3137 MET* 3.2 7.2 + - - +
3157 LYS* 1.3 82.2 - - - +
3177 ILE* 1.3 63.2 + - - +
3197 ALA* 3.9 3.8 + - - +
3207 LEU* 3.8 17.0 + - - +
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Residues in contact with ILE 317 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2757 HIS* 3.8 22.9 - - + +
2787 THR* 4.1 16.6 - - + -
2797 TYR* 5.1 5.8 - - + +
2947 TYR* 4.0 25.1 - - + +
2977 ASN* 3.9 13.5 - - - +
3137 MET* 2.9 28.9 + - + +
3167 GLU* 1.3 76.7 - - - +
3187 THR* 1.3 66.6 + - - +
3197 ALA 3.2 2.0 - - - -
3207 LEU* 3.0 6.3 + - + +
3217 ALA* 2.9 25.3 + - - +
3277 ILE* 3.7 26.9 - - + -
3297 ILE* 3.6 21.1 - - + -
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Residues in contact with THR 318 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3147 GLN* 2.8 30.0 + - - +
3157 LYS* 3.1 30.5 + - + +
3177 ILE* 1.3 71.6 - - - +
3197 ALA* 1.3 59.5 + - - +
3207 LEU 3.1 5.5 + - - -
3217 ALA* 3.1 21.0 + - - +
3237 SER* 5.8 1.0 + - - -
3257 MET 6.1 0.4 - - - +
3277 ILE* 3.7 31.0 - - + -
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Residues in contact with ALA 319 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3157 LYS* 3.5 28.0 + - - +
3167 GLU 4.0 4.7 - - - +
3177 ILE 3.2 1.0 - - - -
3187 THR* 1.3 80.6 + - - +
3207 LEU* 1.3 58.4 + - - +
3217 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