Contacts of the helix formed by residues 308 - 319 (chain 8) 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 8).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2198 VAL* 3.0 19.2 - - - +
2218 LEU* 4.7 5.8 - - - +
3078 PRO* 1.3 73.5 - - - +
3098 ILE* 1.3 63.3 + - - +
3108 ALA* 3.3 3.5 - - - +
3118 ASP* 4.0 21.9 - - - +
3128 ARG* 3.3 21.3 + - - +
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Residues in contact with ILE 309 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1538 LEU* 5.7 4.7 - - + -
2198 VAL* 3.9 15.5 - - + -
2618 LEU* 4.3 14.1 - - + -
2628 PHE* 4.6 8.6 - - + -
2748 ILE* 6.2 2.5 - - + -
2998 MET* 4.3 14.4 - - + -
3038 THR 3.9 7.6 - - - +
3048 THR* 3.2 51.1 - - + +
3068 TYR* 3.2 26.0 - - + +
3078 PRO 3.2 1.8 + - - -
3088 GLY* 1.3 77.2 - - - +
3108 ALA* 1.3 74.2 - - + +
3128 ARG* 3.8 2.8 + - - +
3138 MET* 3.0 32.7 + - + +
3358 ARG* 3.5 13.7 - - - +
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Residues in contact with ALA 310 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2998 MET* 4.0 23.8 - - + -
3088 GLY* 3.3 1.3 - - - +
3098 ILE* 1.3 83.1 - - + +
3118 ASP* 1.4 54.1 + - - +
3138 MET* 3.1 4.3 + - - +
3148 GLN* 2.8 37.2 + - - +
3298 ILE* 4.1 15.0 - - + +
3318 ALA* 4.1 13.0 - - + -
3358 ARG* 5.5 0.7 - - - +
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Residues in contact with ASP 311 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2218 LEU* 3.8 31.2 - - + +
3088 GLY* 3.8 16.2 + - - +
3098 ILE 3.5 0.4 - - - -
3108 ALA* 1.4 73.2 - - - +
3128 ARG* 1.3 66.9 + - - +
3148 GLN* 3.1 11.5 - - - +
3158 LYS* 3.0 26.9 + - - +
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Residues in contact with ARG 312 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2198 VAL* 3.6 12.6 - - + -
2208 ALA 3.0 24.2 + - - +
2218 LEU* 3.8 12.5 - - - +
2228 ASP 4.9 3.5 - - - +
2238 PHE* 2.9 41.7 - - - +
2628 PHE* 3.3 25.6 - - + +
2638 GLN* 3.4 27.5 + - - +
3088 GLY 3.3 15.1 + - - +
3098 ILE 3.9 3.1 - - - +
3118 ASP* 1.3 77.4 - - - +
3138 MET* 1.3 51.8 + - - +
3158 LYS* 3.3 3.7 + - - +
3168 GLU* 2.7 77.6 + - - +
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Residues in contact with MET 313 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1538 LEU* 4.5 8.5 - - + -
2628 PHE* 4.2 11.2 - - + -
2748 ILE* 3.9 17.7 - - + -
2758 HIS* 3.4 35.0 - - - -
2788 THR* 3.0 36.8 - - + +
2978 ASN* 4.4 10.5 - - - +
2998 MET* 4.8 8.7 - - - -
3098 ILE* 3.0 23.4 + - + +
3108 ALA* 3.1 5.1 + - - +
3128 ARG* 1.3 72.8 - - - +
3148 GLN* 1.3 59.3 - - - +
3168 GLU* 3.6 2.1 - - - +
3178 ILE* 2.9 39.0 + - + +
3298 ILE* 4.1 17.5 - - + -
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Residues in contact with GLN 314 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3108 ALA 2.8 12.3 + - - +
3118 ASP* 3.1 16.4 - - - +
3138 MET* 1.3 76.4 - - - +
3158 LYS* 1.3 62.0 - - + +
3188 THR* 2.8 35.0 + - - +
3278 ILE* 3.5 32.4 + - - +
3288 LYS* 4.3 2.0 - - - +
3298 ILE* 3.5 30.4 + - + +
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Residues in contact with LYS 315 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2218 LEU* 6.3 4.7 - - + -
3118 ASP 3.0 12.6 + - - +
3128 ARG* 4.0 3.6 - - - +
3148 GLN* 1.3 82.5 - - + +
3168 GLU* 1.3 66.6 + - - +
3188 THR* 3.1 34.8 + - + +
3198 ALA* 3.5 29.5 - - - +
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Residues in contact with GLU 316 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2628 PHE* 4.6 2.7 - - + -
2758 HIS* 3.2 56.5 + - + -
3128 ARG* 2.7 60.0 + - - +
3138 MET* 3.2 7.6 + - - +
3158 LYS* 1.3 83.0 - - - +
3178 ILE* 1.3 62.7 + - - +
3198 ALA* 3.9 4.0 + - - +
3208 LEU* 3.8 17.3 + - - +
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Residues in contact with ILE 317 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2758 HIS 3.8 22.4 - - - +
2788 THR* 4.1 16.4 - - + -
2798 TYR* 5.1 5.8 - - + +
2948 TYR* 4.0 25.4 - - + +
2978 ASN* 3.9 14.1 - - - +
3138 MET* 2.9 28.8 + - + +
3168 GLU* 1.3 76.3 - - - +
3188 THR* 1.3 66.6 + - - +
3198 ALA 3.2 1.6 - - - -
3208 LEU* 3.0 6.9 + - + +
3218 ALA* 2.9 24.9 + - - +
3278 ILE* 3.7 26.2 - - + -
3298 ILE* 3.6 20.4 - - + -
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Residues in contact with THR 318 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3148 GLN* 2.8 30.8 + - - +
3158 LYS* 3.1 31.4 + - + +
3178 ILE* 1.3 73.7 - - - +
3198 ALA* 1.3 60.7 + - - +
3208 LEU 3.1 5.4 + - - -
3218 ALA* 3.1 21.3 + - - +
3238 SER* 5.8 0.9 + - - -
3258 MET 6.1 0.4 - - - +
3278 ILE* 3.7 29.4 - - + -
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Residues in contact with ALA 319 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3158 LYS* 3.5 28.0 + - - +
3168 GLU* 4.0 4.7 - - - +
3178 ILE 3.2 0.4 - - - -
3188 THR* 1.3 79.9 + - - +
3208 LEU* 1.3 59.5 + - - +
3218 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